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‎HCV1a.json‎

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{
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"bco_id": "https://github.com/biocompute-objects/BCO_Specification/blob/master/HCV1a.json",
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"digital_signature": "0B61E7C0EFF537CADADE475AA6386262FCDBC4DC",
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"bco_spec_version" : "https://w3id.org/biocompute/spec/v1.2",
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"provenance_domain": {
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"name": "HCV1a ledipasvir resistance SNP detection",
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"version": "2.9",
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"review": [
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{
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"status": "approved",
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"reviewer_comment": "Approved by GW staff. Waiting for approval from FDA Reviewer",
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"reviewer": {
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"name": "Charles Hadley King",
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"affiliation": "George Washington University",
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"email": "[email protected]",
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"contribution": ["curatedBy"],
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"orcid": "https://orcid.org/0000-0003-1409-4549"
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}
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},
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{
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"status": "approved",
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"reviewer_comment": "The revised BCO looks fine",
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"reviewer": {
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"name": "Eric Donaldson",
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"affiliation": "FDA",
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"email": "[email protected]",
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"contribution": ["curatedBy"]
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}
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}
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],
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"obsolete_after" : "2118-09-26T14:43:43-0400",
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"embargo" : {
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"start_time": "2000-09-26T14:43:43-0400",
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"end_time": "2000-09-26T14:43:45-0400"
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},
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"created": "2017-01-24T09:40:17-0500",
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"modified": "2018-09-21T14:06:14-0400",
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"contributors": [
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{
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"name": "Charles Hadley King",
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"affiliation": "George Washington University",
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"email": "[email protected]",
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"contribution": ["createdBy", "curatedBy"],
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"orcid": "https://orcid.org/0000-0003-1409-4549"
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},
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{
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"name": "Eric Donaldson",
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"affiliation": "FDA",
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"email": "[email protected]",
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"contribution": ["authoredBy"]
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}
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],
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"license": "https://spdx.org/licenses/CC-BY-4.0.html"
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},
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"usability_domain": [
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"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]",
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"Identify treatment emergent amino acid (substitutions)[SO:1000002] that correlate with antiviral drug treatment failure",
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"Determine whether the treatment emergent amino acid (substitutions)[SO:1000002] identified correlate with treatment failure involving other drugs against the same virus",
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"GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
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],
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"extension_domain":{
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"fhir_extension": [
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{
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"fhir_endpoint": "http://fhirtest.uhn.ca/baseDstu3",
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"fhir_version": "3",
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"fhir_resources": [
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{
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"fhir_resource": "Sequence",
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"fhir_id": "21376"
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},
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{
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"fhir_resource": "DiagnosticReport",
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"fhir_id": "6288583"
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},
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{
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"fhir_resource": "ProcedureRequest",
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"fhir_id": "25544"
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},
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{
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"fhir_resource": "Observation",
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"fhir_id": "92440"
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},
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{
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"fhir_resource": "FamilyMemberHistory",
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"fhir_id": "4588936"
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}
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]
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}
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],
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"scm_extension": {
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"scm_repository": "https://github.com/example/repo1",
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"scm_type": "git",
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"scm_commit": "c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21",
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"scm_path": "workflow/hive-viral-mutation-detection.cwl",
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"scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
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}
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},
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"description_domain": {
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"keywords": [
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"HCV1a",
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"Ledipasvir",
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"antiviral resistance",
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"SNP",
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"amino acid substitutions"
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],
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"xref": [
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{
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"namespace": "pubchem.compound",
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"name": "PubChem-compound",
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"ids": ["67505836"],
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"access_time": "2018-13-02T10:15-05:00"
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},
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{
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"namespace": "pubmed",
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"name": "PubMed",
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"ids": ["26508693"],
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"access_time": "2018-13-02T10:15-05:00"
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},
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{
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"namespace": "so",
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"name": "Sequence Ontology",
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"ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"],
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"access_time": "2018-13-02T10:15-05:00"
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},
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{
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"namespace": "taxonomy",
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"name": "Taxonomy",
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"ids": ["31646"],
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"access_time": "2018-13-02T10:15-05:00"
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}
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],
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"platform": ["HIVE"],
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"pipeline_steps": [
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{
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"step_number": 1,
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"name": "HIVE-hexagon",
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"description": "Alignment of reads to a set of references",
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"version": "1.3",
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"prerequisite": [
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{
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"name": "Hepatitis C virus genotype 1",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus type 1b complete genome",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus clone J8CF, complete genome",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus S52 polyprotein gene",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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],
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"input_list": [
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{
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"address": "http://example.com/dna.cgi?cmd=objFile&ids=514683",
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"access_time": "2017-01-24T09:40:17-0500"
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},
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{
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"address": "http://example.com/dna.cgi?cmd=objFile&ids=514682",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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],
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"output_list": [
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{
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"address": "http://example.com/data/514769/allCount-aligned.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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]
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},
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{
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"step_number": 2,
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"name": "HIVE-heptagon",
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"description": "variant calling",
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"version": "1.3",
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"input_list": [
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{
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"address": "http://example.com/data/514769/dnaAccessionBased.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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],
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"output_list": [
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{
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"address": "http://example.com/data/514801/SNPProfile.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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},
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{
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"address": "http://example.com/data/14769/allCount-aligned.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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]
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}
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]
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},
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"execution_domain": {
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"script_access_type": "URI",
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"script": ["https://example.com/workflows/antiviral_resistance_detection_hive.py"],
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"script_driver": "shell",
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"software_prerequisites": [
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{
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"name": "HIVE-hexagon",
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"version": "babajanian.1",
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"uri": {
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"address": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
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"access_time": "2017-01-24T09:40:17-0500",
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"sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c"
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}
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},
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{
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"name": "HIVE-heptagon",
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"version": "albinoni.2",
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"uri": {
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"address": "http://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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],
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"external_data_endpoints": [
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{
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"name": "HIVE",
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"url": "http://example.com/dna.cgi?cmd=login"
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},
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{
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"name": "access to e-utils",
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"url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
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}
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],
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"env_parameters": {
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"key": "HOSTTYPE",
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"value" : "x86_64-linux"
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}
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},
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"parametric_domain": [
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{"param": "seed", "value": "14", "step": "1"},
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{"param":"minimum_match_len", "value": "66", "step": "1"},
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{"param": "divergence_threshold_percent", "value": 0.30, "step": "1"},
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{"param": "minimum_coverage", "value": "15", "step": "2"},
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{"param": "freq_cutoff", "value": 0.10, "step": "2"}
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],
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"io_domain": {
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"input_subdomain": [
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{
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"name": "Hepatitis C virus genotype 1",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus type 1b complete genome",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus clone J8CF, complete genome",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "Hepatitis C virus S52 polyprotein gene",
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"uri": {
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"address": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "HCV1a_drug_resistant_sample0001-01",
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"uri": {
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"address": "http://example.com/nuc-read/514682",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "HCV1a_drug_resistant_sample0001-02",
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"uri": {
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"address": "http://example.com/nuc-read/514683",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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],
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"output_subdomain": [
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{
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"mediatype": "text/csv",
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"uri": {
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"address": "http://example.com/data/514769/dnaAccessionBased.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"mediatype": "text/csv",
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"uri": {
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"address": "http://example.com/data/514801/SNPProfile*.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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]
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},
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"error_domain": {
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"empirical_error": {
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"false_negative_alignment_hits": "<0.0010",
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"false_discovery": "<0.05"
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},
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"algorithmic_error": {
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"false_positive_mutation_calls_discovery": "<0.00005",
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"false_discovery": "0.005"
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}
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}
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}

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