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add examples
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HadleyKing committed Dec 17, 2018
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{
"bco_id": "https://w3id.org/biocompute/1.3.0/examples/HCV1a.json",
"checksum": "06DACE70679F35BA87A3DD6FFFED4ED24A4F5B8C2571264C37E5F1B3ADE04A31",
"bco_spec_version" : "https://w3id.org/biocompute/1.3.0/",
"provenance_domain": {
"name": "HCV1a ledipasvir resistance SNP detection",
"version": "2.9",
"review": [
{
"status": "approved",
"reviewer_comment": "Approved by GW staff. Waiting for approval from FDA Reviewer",
"date": "2017-11-12T12:30:48-0400",
"reviewer": {
"name": "Charles Hadley King",
"affiliation": "George Washington University",
"email": "[email protected]",
"contribution": ["curatedBy"],
"orcid": "https://orcid.org/0000-0003-1409-4549"
}
},
{
"status": "approved",
"reviewer_comment": "The revised BCO looks fine",
"date": "2017-12-12T12:30:48-0400",
"reviewer": {
"name": "Eric Donaldson",
"affiliation": "FDA",
"email": "[email protected]",
"contribution": ["curatedBy"]
}
}
],
"obsolete_after" : "2118-09-26T14:43:43-0400",
"embargo" : {
"start_time": "2000-09-26T14:43:43-0400",
"end_time": "2000-09-26T14:43:45-0400"
},
"created": "2017-01-24T09:40:17-0500",
"modified": "2018-09-21T14:06:14-0400",
"contributors": [
{
"name": "Charles Hadley King",
"affiliation": "George Washington University",
"email": "[email protected]",
"contribution": ["createdBy", "curatedBy"],
"orcid": "https://orcid.org/0000-0003-1409-4549"
},
{
"name": "Eric Donaldson",
"affiliation": "FDA",
"email": "[email protected]",
"contribution": ["authoredBy"]
}
],
"license": "https://spdx.org/licenses/CC-BY-4.0.html"
},
"usability_domain": [
"Identify baseline single nucleotide polymorphisms (SNPs)[SO:0000694], (insertions)[SO:0000667], and (deletions)[SO:0000045] that correlate with reduced (ledipasvir)[pubchem.compound:67505836] antiviral drug efficacy in (Hepatitis C virus subtype 1)[taxonomy:31646]",
"Identify treatment emergent amino acid (substitutions)[SO:1000002] that correlate with antiviral drug treatment failure",
"Determine whether the treatment emergent amino acid (substitutions)[SO:1000002] 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"
],
"extension_domain":{
"fhir_extension": [
{
"fhir_endpoint": "http://fhirtest.uhn.ca/baseDstu3",
"fhir_version": "3",
"fhir_resources": [
{
"fhir_resource": "Sequence",
"fhir_id": "21376"
},
{
"fhir_resource": "DiagnosticReport",
"fhir_id": "6288583"
},
{
"fhir_resource": "ProcedureRequest",
"fhir_id": "25544"
},
{
"fhir_resource": "Observation",
"fhir_id": "92440"
},
{
"fhir_resource": "FamilyMemberHistory",
"fhir_id": "4588936"
}
]
}
],
"scm_extension": {
"scm_repository": "https://github.com/example/repo1",
"scm_type": "git",
"scm_commit": "c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21",
"scm_path": "workflow/hive-viral-mutation-detection.cwl",
"scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
}
},
"description_domain": {
"keywords": [
"HCV1a",
"Ledipasvir",
"antiviral resistance",
"SNP",
"amino acid substitutions"
],
"xref": [
{
"namespace": "pubchem.compound",
"name": "PubChem-compound",
"ids": ["67505836"],
"access_time": "2018-13-02T10:15-05:00"
},
{
"namespace": "pubmed",
"name": "PubMed",
"ids": ["26508693"],
"access_time": "2018-13-02T10:15-05:00"
},
{
"namespace": "so",
"name": "Sequence Ontology",
"ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"],
"access_time": "2018-13-02T10:15-05:00"
},
{
"namespace": "taxonomy",
"name": "Taxonomy",
"ids": ["31646"],
"access_time": "2018-13-02T10:15-05:00"
}
],
"platform": ["HIVE"],
"pipeline_steps": [
{
"step_number": 1,
"name": "HIVE-hexagon",
"description": "Alignment of reads to a set of references",
"version": "1.3",
"prerequisite": [
{
"name": "Hepatitis C virus genotype 1",
"uri": {
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus type 1b complete genome",
"uri": {
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": {
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus clone J8CF, complete genome",
"uri": {
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus S52 polyprotein gene",
"uri": {
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24T09:40:17-0500"
}
}
],
"input_list": [
{
"uri": "http://example.com/dna.cgi?cmd=objFile&ids=514683",
"access_time": "2017-01-24T09:40:17-0500"
},
{
"uri": "http://example.com/dna.cgi?cmd=objFile&ids=514682",
"access_time": "2017-01-24T09:40:17-0500"
}
],
"output_list": [
{
"uri": "http://example.com/data/514769/allCount-aligned.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
},
{
"step_number": 2,
"name": "HIVE-heptagon",
"description": "variant calling",
"version": "1.3",
"input_list": [
{
"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
],
"output_list": [
{
"uri": "http://example.com/data/514801/SNPProfile.csv",
"access_time": "2017-01-24T09:40:17-0500"
},
{
"uri": "http://example.com/data/14769/allCount-aligned.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
}
]
},
"execution_domain": {
"script":[
{
"uri": {
"uri": "https://example.com/workflows/antiviral_resistance_detection_hive.py"
}
}
],
"script_driver": "shell",
"software_prerequisites": [
{
"name": "HIVE-hexagon",
"version": "babajanian.1",
"uri": {
"uri": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500",
"sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c"
}
},
{
"name": "HIVE-heptagon",
"version": "albinoni.2",
"uri": {
"uri": "http://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500"
}
}
],
"external_data_endpoints": [
{
"name": "HIVE",
"url": "http://example.com/dna.cgi?cmd=login"
},
{
"name": "access to e-utils",
"url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
}
],
"environment_variables": {
"HOSTTYPE": "x86_64-linux",
"EDITOR": "vim"
}
},
"parametric_domain": [
{"param": "seed", "value": "14", "step": "1"},
{"param":"minimum_match_len", "value": "66", "step": "1"},
{"param": "divergence_threshold_percent", "value": "0.30", "step": "1"},
{"param": "minimum_coverage", "value": "15", "step": "2"},
{"param": "freq_cutoff", "value": "0.10", "step": "2"}
],
"io_domain": {
"input_subdomain": [
{
"uri": {
"filename": "Hepatitis C virus genotype 1",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus type 1b complete genome",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus S52 polyprotein gene",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "HCV1a_drug_resistant_sample0001-01",
"uri": "http://example.com/nuc-read/514682",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{

"uri": {
"filename": "HCV1a_drug_resistant_sample0001-02",
"uri": "http://example.com/nuc-read/514683",
"access_time": "2017-01-24T09:40:17-0500"
}
}
],
"output_subdomain": [
{
"mediatype": "text/csv",
"uri": {
"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"mediatype": "text/csv",
"uri": {
"uri": "http://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
}
]
},
"error_domain": {
"empirical_error": {
"false_negative_alignment_hits": "<0.0010",
"false_discovery": "<0.05"
},
"algorithmic_error": {
"false_positive_mutation_calls_discovery": "<0.00005",
"false_discovery": "0.005"
}
}
}
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