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Merge pull request #33 from ELIXIR-Belgium/dev
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Dev
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@vdkkia
vdkkia authored Feb 9, 2022
2 parents a24b6eb + 6cb4f53 commit 0ee5e29
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24 changes: 24 additions & 0 deletions Attribute type possibilities.txt
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String
Date time
Date
Real number
Integer
Web link
Email address
Text
ChEBI
ECN
MetaNEtX chemical
MetaNEtX reaction
MetaNEtX compartment
InChi
Boolean
SEEK Strain
SEEK Sample
SEEK Sample Multi
Controlled Vocabulary
Ontology
URI
DOI
NCBI ID
SEEK Data file
150 changes: 104 additions & 46 deletions .../older versions/all_organisms_v1.0.0.json → ...study templates/all_organisms_v1.2.0.json
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[
{
"metadata": {
"name": "all organisms",
"group": "ena",
"group_order": 1,
"temporary_name": "1_ena_all_organisms",
"template_version": "1.2.0",
"isa_config": "genome_seq_default_v2015-07-02",
"isa_measurement_type": "genome sequencing",
"isa_technology_type": "nucleotide sequencing",
"isa_protocol_type": "sample collection",
"repo_schema_id": "ERC000011.xml 2021",
"organism": "any",
"level": "study"
},
"data": [
{
"name": "Source Name",
"description": "Sources are considered as the starting biological material used in a study.",
"dataType": "String",
"required": "true"
"required": "true",
"isaTag": "source"
},
{
"name": "tax_id", //First field on an ENA sample file. Might want to add ontology to it and restrict dataType to integers.
"description": "NCBI Taxonomy Identifier. This is appropriate for individual organisms and some environmental samples.",
"dataType": "Ontology term",
"required": "true"
"name": "tax_id", //First field on an ENA sample file. It is the number ID
"description": "NCBI Taxonomy Identifier number ID. This is appropriate for individual organisms and some environmental samples.",
"dataType": "String",
"required": true,
"ontology": null,
"isaTag": "source_characteristic"
},
{
"name": "organism",
"description": "Provide a taxonomic information associated to the Source Biological material (for example, Species, genus, strain,....). Ideally, provide NCBI TaxID or NEWT identifier",
"dataType": "Ontology term",
"required": "false",
"ontology": [
{ "name": "NEWT UniProt Taxonomy Database", "version": "Jun 2010", "abbreviation": "NEWT", "id": "" }
]
"description": "Provide a taxonomic information associated to the Source Biological material (for example, Species, genus, strain,....). Ideally, provide NCBI TaxID or NEWT identifier", //Changed to the description from ENA
"dataType": "String",
"required": false,
"ontology": null,
"isaTag": "source_characteristic"
},
{
"name": "cell_type",
"description": "cell type from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "dev_stage",
"description": "if the sample was obtained from an organism in a specific developmental stage, it is specified with this qualifier",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "germline",
"description": "the sample described presented in the entry has not undergone somatic genomic rearrangement as part of an adaptive immune response; it is the unrearranged molecule that was inherited from the parental germline",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "tissue_lib",
"description": "tissue library from which sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "tissue_type",
"description": "tissue type from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "collection_date",
"description": "date that the specimen was collected",
"dataType": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$",
"required": false,
"ontology": null,
"dataType": "^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$"
"isaTag": "source_characteristic"
},
{
"name": "isolation_source",
"description": "describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "lat_lon",
"description": "geographical coordinates of the location where the specimen was collected",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "collected_by",
"description": "name of persons or institute who collected the specimen",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "geographic location (country and/or sea)",
"description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).",
"required": false,
"ontology": "http://insdc.org/country.html",
"dataType": "string",
"required": false,
"ontology": null,
"CVList": [
"Afghanistan",
"Albania",
Expand Down Expand Up @@ -369,153 +395,185 @@
"not collected",
"not provided",
"restricted access"
]
],
"isaTag": "source_characteristic"
},
{
"name": "geographic location (region and locality)",
"description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "identified_by",
"description": "name of the expert who identified the specimen taxonomically",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "environmental_sample",
"description": "identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string",
"CVList": ["No", "Yes"]
"CVList": ["No", "Yes"],
"isaTag": "source_characteristic"
},
{
"name": "mating_type",
"description": "mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "sex",
"description": "sex of the organism from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "lab_host",
"description": "scientific name of the laboratory host used to propagate the source organism from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "host scientific name",
"description": "Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "bio_material",
"description": "identifier for the biological material from which the sample was obtained, with optional institution code and collection code for the place where it is currently stored.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "culture_collection",
"description": "institution code and identifier for the culture from which the sample was obtained, with optional collection code.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "specimen_voucher",
"description": "identifier for the specimen from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "cultivar",
"description": "cultivar (cultivated variety) of plant from which sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "ecotype",
"description": "a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "isolate",
"description": "individual isolate from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "sub_species",
"description": "name of sub-species of organism from which sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "variety",
"description": "variety (= varietas, a formal Linnaean rank) of organism from which sample was derived.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "sub_strain",
"description": "name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "cell_line",
"description": "cell line from which the sample was obtained",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "serotype",
"description": "serological variety of a species characterized by its antigenic properties",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "serovar",
"description": "serological variety of a species (usually a prokaryote) characterized by its antigenic properties",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "strain",
"description": "Name of the strain from which the sample was obtained.",
"dataType": "string",
"required": false,
"ontology": null,
"dataType": "string"
"isaTag": "source_characteristic"
},
{
"name": "sample collection",
"description": "type of assay or experimental step performed.",
"dataType": "string",
"required": true,
"ontology": null,
"CVList":,//SOPtittle
"isaTag": "protocol"
},
{
"name": "Sample Name",
"description": "Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.",
"dataType": "String",
"required": "true"
"required": true,
"isaTag": "sample"
}
]
}
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