Skip to content

Commit

Permalink
schema update
Browse files Browse the repository at this point in the history 
Schema update
  • Loading branch information
@HadleyKing
HadleyKing committed Jun 27, 2019
1 parent a8b578d commit 86d5725
Show file tree
Hide file tree
Showing 15 changed files with 1,639 additions and 1,364 deletions.
Binary file added .DS_Store
View file
Binary file not shown.
28 changes: 21 additions & 7 deletions 10_SCA1/bcoexample_10.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,11 @@
"version": "1.0",
"createdby": "[email protected]",
"created": "Feb 02, 2017 11:11:00",
"modified": "Feb 23, 2017 15:42:38",
"modified": "Feb 23, 2017 15:42:38",
"authors": [
{"orcid": "0000-0003-1409-4549"},
{"orcid": "0000-0002-9920-565X"}
],
"digital_signature": "",
"verification_status": "unreviewed",
"publication_status": "draft",
Expand All @@ -18,10 +22,6 @@
"Full-penetrance: 39 and above CAG trinucleotide repeats."
],
"description_domain": {
"authors": [
{"orchid": "0000-0003-1409-4549"},
{"orchid": "0000-0002-9920-565X"}
],
"xref":[
"taxID:9606",
"DO:0050954",
Expand Down Expand Up @@ -69,10 +69,24 @@
"pipeline_version": "0.2",
"script": "https://hive.biochemistry.gwu.edu/workflows/antiviral_resistance_detection_hive.sh",
"driver": "//hive.biochemistry.gwu.edu/hive-driver",
"prerequisites": [
"software_prerequisites": [
{"name":"HIVE_hexagon","version":"1.3"},
{"name":"HIVE_heptagon","version":"1.3"}
]
],
"domain_prerequisites": [
{
"url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/",
"name": "access to e-utils"
},
{
"url": "ftp://:22/",
"name": "access to ftp"
}
],
"env_parameters": [
"HIVEv1.3"
],
"script_type": "URI"
},
"parametric_domain": {
"trinucleotide_count_file": "36"
Expand Down
266 changes: 131 additions & 135 deletions 1_HCV1a/bcoexample_1.json
View file
Original file line number Diff line number Diff line change
@@ -1,136 +1,132 @@
{
"id": "obj.1270",
"name": "HCV1a [taxID:31646] ledipasvir [PubChem:67505836] resistance SNP [SO:0000694] detection",
"version": "1.1",
"createdby": "[email protected]",
"created": "Jan 24, 2017 09:40:17",
"modified": "Jun 22, 2017 14:47:49",
"digital_signature": "905d7fce3f3ac64c8ea86f058ca71658",
"verification_status": "unreviewed",
"publication_status": "draft",
"usability_domain": [
"Identify baseline single nucleotide polymorphisms SNPs [SO:0000694], insertions [SO:0000667], and deletions [SO:0000045] that correlate with reduced ledipasvir [PubChem:67505836] antiviral drug efficacy in Hepatitis C virus subtype 1 [taxID:31646]",
"Identify treatment emergent amino acid substitutions [SO:0000048] that correlate with antiviral drug treatment failure",
"Determine whether the treatment emergent amino acid substitutions [SO:0000048] identified correlate with treatment failure involving other drugs against the same virus",
"GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
],
"authors": [
{
"orcid": "0000-0003-1409-4549"
},
{
"name": "Eric Donaldson"
}
],
"description_domain": {
"keywords": [
"HCV1a",
"Ledipasvir",
"antiviral resistance",
"SNP",
"amino acid substitutions"
"test2"
],
"xref": [
"SO:0000694",
"SO:0000667",
"SO:0000045",
"PubChem:67505836",
"SO:0000048",
"taxID:31646",
"PMID:25123381",
"PMID:26508693"
],
"pipeline_steps": [
{
"tool_name": "HIVE-hexagon",
"tool_desc": "The tool is used for alignment of reads to a set of references",
"tool_version": "1.3",
"tool_package": "HIVE",
"step_number": "1",
"input_uri_list": [
"https://www.ncbi.nlm.nih.gov/nuccore/NC_004102.1",
"https://www.ncbi.nlm.nih.gov/nuccore/AJ238799.1",
"https://hive/nuc-read/557406",
"https://hive/nuc-read/557407"
],
"output_uri_list": [
"https://hive/data/557413/allCount-aligned.csv"
]
},
{
"tool_name": "HIVE-heptagon",
"tool_desc": "This tool is used for variant calling",
"tool_version": "1.3",
"tool_package": "HIVE",
"step_number": "2",
"input_uri_list": [
"https://hive/data/557413/allCount-aligned.csv"
],
"output_uri_list": [
"https://hive/data/557416/SNPProfile.csv"
]
}
]
},
"execution_domain": {
"script": "https://hive.biochemistry.gwu.edu/workflows/antiviral_resistance_detection_hive.sh",
"pipeline_version": "2.0",
"platform": "HIVE",
"driver": "shell",
"prerequisites": [
"name:HIVE-hexagon",
"version:1.3 ",
"name:HIVE-heptagon",
"version:1.3"
],
"env_parameters": [
"HIVEv1.3"
],
"script_type": "URI"
},
"parametric_domain": {
"heptagon_divergence_threshold_percent": "30",
"hexagon_minimum_coverage": "15",
"hexagon_seed": "14",
"heptagon_freq_cutoff": "0.10",
"hexagon_minimum_match_len": "66"
},
"io_domain": {
"reference_uri_list": [
"https://www.ncbi.nlm.nih.gov/nuccore/NC_004102.1",
"https://www.ncbi.nlm.nih.gov/nuccore/AJ238799.1"
],
"input_uri_list": [
"https://hive/data/nuc-read/557406",
"https://hive/data/nuc-read/557407",
"https://hive/data/557413/allCount-aligned.csv"
],
"output_uri_list": [
"https://hive/data/557413/allCount-aligned.csv",
"https//hive/data/557416/SNPProfile.csv"
],
"output_subdomain": [
"hit_list ",
"title:hit list",
"nuri:https://hive/data/557413/allCount-aligned.csv",
"mime-type:csv",
"mutation_profile:",
"title:mutation profile",
"uri:https//hive/data/557416/SNPProfile.csv",
"mime-type:csv"
],
"input_subdomain": [
"Read_Files:",
"https://hive/data/nuc-read/557406",
"https://hive/data/nuc-read/557407",
"HCV1a_reference_genome",
"https://www.ncbi.nlm.nih.gov/nuccore/NC_004102.1",
"https://www.ncbi.nlm.nih.gov/nuccore/AJ238799.1"
]
},
"error_domain": [
"false negative alignment hits < 0.0010",
"false positive mutation calls discovery < 0.0005"
]
}
"id": "obj.1270",
"name": "HCV1a [taxonomy:31646] ledipasvir [PubChem:67505836] resistance SNP [so:0000694] detection",
"structured_name": "HCV1a [taxonomy:31646] ledipasvir [PubChem:67505836] resistance SNP [so:0000694] detection",
"version": "1.1",
"createdby": "[email protected]",
"created": "Jan 24, 2017 09:40:17",
"modified": "Jun 25, 2019 14:47:49",
"digital_signature": "905d7fce3f3ac64c8ea86f058ca71658",
"verification_status": "unreviewed",
"publication_status": "draft",
"usability_domain": [
"Identify baseline single nucleotide polymorphisms SNPs [so:0000694], insertions [so:0000667], and deletions [so:0000045] that correlate with reduced ledipasvir [PubChem:67505836] antiviral drug efficacy in Hepatitis C virus subtype 1 [taxonomy:31646]",
"Identify treatment emergent amino acid substitutions [so:0000048] that correlate with antiviral drug treatment failure",
"Determine whether the treatment emergent amino acid substitutions [so:0000048] identified correlate with treatment failure involving other drugs against the same virus",
"GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
],
"authors": [
{
"orcid": "0000-0003-1409-4549"
},
{
"name": "Eric Donaldson"
}
],
"description_domain": {
"keywords": [
"HCV1a",
"Ledipasvir",
"antiviral resistance",
"SNP",
"amino acid substitutions"
],
"xref": [
"so:0000694",
"so:0000667",
"so:0000045",
"PubChem:67505836",
"so:0000048",
"taxonomy:31646",
"pubmed:25123381",
"pubmed:26508693"
],
"pipeline_steps": [
{
"tool_name": "HIVE-hexagon",
"tool_desc": "The tool is used for alignment of reads to a set of references",
"tool_version": "1.3",
"tool_package": "HIVE",
"step_number": "1",
"input_uri_list": [
"https://www.ncbi.nlm.nih.gov/nuccore/NC_004102.1",
"https://www.ncbi.nlm.nih.gov/nuccore/AJ238799.1",
"https://hive/nuc-read/557406",
"https://hive/nuc-read/557407"
],
"output_uri_list": [
"https://hive/data/557413/allCount-aligned.csv"
]
},
{
"tool_name": "HIVE-heptagon",
"tool_desc": "This tool is used for variant calling",
"tool_version": "1.3",
"tool_package": "HIVE",
"step_number": "2",
"input_uri_list": [
"https://hive/data/557413/allCount-aligned.csv"
],
"output_uri_list": [
"https://hive/data/557416/SNPProfile.csv"
]
}
]
},
"execution_domain": {
"script": "https://hive.biochemistry.gwu.edu/workflows/antiviral_resistance_detection_hive.sh",
"pipeline_version": "2.0",
"platform": "HIVE",
"driver": "shell",
"software_prerequisites": [
{
"name": "HIVE_hexagon",
"version": "1.3"
},
{
"name": "HIVE_heptagon",
"version": "1.3"
}
],
"domain_prerequisites": [
{
"url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/",
"name": "access to e-utils"
},
{
"url": "ftp://:22/",
"name": "access to ftp"
}
],
"env_parameters": [
"HIVEv1.3"
],
"script_type": "URI"
},
"parametric_domain": {
"heptagon_divergence_threshold_percent": "30",
"hexagon_minimum_coverage": "15",
"hexagon_seed": "14",
"heptagon_freq_cutoff": "0.10",
"hexagon_minimum_match_len": "66"
},
"io_domain": {
"reference_uri_list": [
"https://www.ncbi.nlm.nih.gov/nuccore/NC_004102.1",
"https://www.ncbi.nlm.nih.gov/nuccore/AJ238799.1"
],
"input_uri_list": [
"https://hive/data/nuc-read/557406",
"https://hive/data/nuc-read/557407",
"https://hive/data/557413/allCount-aligned.csv"
],
"output_uri_list": [
"https://hive/data/557413/allCount-aligned.csv",
"https//hive/data/557416/SNPProfile.csv"
]
},
"error_domain": [
"false negative alignment hits < 0.0010",
"false positive mutation calls discovery < 0.0005"
]
}
Loading

0 comments on commit 86d5725

Please sign in to comment.