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 {     "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HCV1a.json",     "etag": "11ee4c3b8a04ad16dcca19a6f478c0870d3fe668ed6454096ab7165deb1ab8ea",     "spec_version": "https://w3id.org/ieee/ieee-2791-schema/",     "provenance_domain": {         "name": "HCV1a ledipasvir resistance SNP detection",         "version": "2.9",         "review": [             {                 "status": "approved",                 "revi..."

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Created page with "<pre> { "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HCV1a.json", "etag": "11ee4c3b8a04ad16dcca19a6f478c0870d3fe668ed6454096ab7165deb1ab8ea", "spec_version": "https://w3id.org/ieee/ieee-2791-schema/", "provenance_domain": { "name": "HCV1a ledipasvir resistance SNP detection", "version": "2.9", "review": [ { "status": "approved", "revi..."

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<pre>
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"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",
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"name": "Charles Hadley King",
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"date": "2017-12-12T12:30:48-0400",
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"modified": "2018-09-21T14:06:14-0400",
"contributors": [
{
"name": "Charles Hadley King",
"affiliation": "George Washington University",
"email": "hadley_king@gwu.edu",
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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]",
"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",
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"fhir_version": "3",
"fhir_resources": [
{
"fhir_resource": "Sequence",
"fhir_id": "21376"
},
{
"fhir_resource": "DiagnosticReport",
"fhir_id": "6288583"
},
{
"fhir_resource": "ProcedureRequest",
"fhir_id": "25544"
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"fhir_resource": "Observation",
"fhir_id": "92440"
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"Ledipasvir",
"antiviral resistance",
"SNP",
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"name": "PubChem-compound",
"ids": [
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"access_time": "2017-01-24T09:40:17-0500"
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}
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{
"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
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"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": [
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}
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},
{
"step_number": 2,
"name": "HIVE-heptagon",
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"version": "1.3",
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}
],
"output_list": [
{
"uri": "http://example.com/data/514801/SNPProfile.csv",
"access_time": "2017-01-24T09:40:17-0500"
},
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"access_time": "2017-01-24T09:40:17-0500"
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}
]
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],
"script_driver": "shell",
"software_prerequisites": [
{
"name": "HIVE-hexagon",
"version": "babajanian.1",
"uri": {
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"access_time": "2017-01-24T09:40:17-0500",
"sha1_checksum": "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"
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},
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"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": {
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"false_discovery": "<0.05"
},
"algorithmic_error": {
"false_positive_mutation_calls_discovery": "<0.00005",
"false_discovery": "0.005"
}
}
}
</pre>

HCV1a ledipasvir resistance SNP detection - Revision history