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HadleyKingHadleyKing
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Updat to HCV
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‎HCV1a.json‎

Lines changed: 47 additions & 44 deletions
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@@ -1,14 +1,15 @@
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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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"bco_id": "https://w3id.org/biocompute/examples/HCV1a.json",
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"checksum": "22B641C02C06553F00310A0E6816070FE2988476B7BC13BF87A2C286A7DE3583",
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"bco_spec_version" : "https://w3id.org/biocompute/spec/1.3.0",
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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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"date": "2017-11-12T12:30:48-0400",
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"reviewer": {
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"name": "Charles Hadley King",
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"affiliation": "George Washington University",
@@ -20,6 +21,7 @@
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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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"date": "2017-12-12T12:30:48-0400",
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"reviewer": {
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"name": "Eric Donaldson",
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"affiliation": "FDA",
@@ -140,52 +142,52 @@
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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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"uri": "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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"uri": "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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"uri": "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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"uri": "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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"uri": "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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"uri": "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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"uri": "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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"uri": "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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]
@@ -197,33 +199,34 @@
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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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"uri": "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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"uri": "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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"uri": "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": {
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"uri": "https://example.com/workflows/antiviral_resistance_detection_hive.py"
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},
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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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"uri": "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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}
@@ -232,7 +235,7 @@
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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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"uri": "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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}
@@ -247,66 +250,66 @@
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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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"environment_variables": {
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"HOSTTYPE": "x86_64-linux",
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"EDITOR": "vim"
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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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"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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"filename": "Hepatitis C virus genotype 1",
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"uri": "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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"filename": "Hepatitis C virus type 1b complete genome",
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"uri": "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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"filename": "Hepatitis C virus (isolate JFH-1) genomic RNA",
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"uri": "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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"uri": "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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"filename": "Hepatitis C virus S52 polyprotein gene",
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"uri": "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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"filename": "HCV1a_drug_resistant_sample0001-01",
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"uri": "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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"filename": "HCV1a_drug_resistant_sample0001-02",
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"uri": "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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}
@@ -315,14 +318,14 @@
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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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"uri": "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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"uri": "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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