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In this vignette, we will use the biocompute package to recreate the example Biocompute Object (HCV1a.json) used in the BCO specification.
library("biocompute")name <- "HCV1a ledipasvir resistance SNP detection"
version <- "1.0.0"
review <- data.frame(
"status" = c("approved", "approved"),
"reviewer_comment" = c("Approved by [company name] staff. Waiting for approval from FDA Reviewer", "The revised BCO looks fine"),
"date" = c(
as.POSIXct("2017-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-12-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "America/Los_Angeles")
),
"reviewer_name" = c("Jane Doe", "John Doe"),
"reviewer_affiliation" = c("Seven Bridges Genomics", "U.S. Food and Drug Administration"),
"reviewer_email" = c("example@sevenbridges.com", "example@fda.gov"),
"reviewer_contribution" = c("curatedBy", "curatedBy"),
"reviewer_orcid" = c("https://orcid.org/0000-0000-0000-0000", NA),
stringsAsFactors = FALSE
)
derived_from <- "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json"
obsolete_after <- as.POSIXct("2018-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
embargo <- c(
"start_time" = as.POSIXct("2017-10-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
"end_time" = as.POSIXct("2017-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
)
created <- as.POSIXct("2017-01-20T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
modified <- as.POSIXct("2019-05-10T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
contributors <- data.frame(
"name" = c("Jane Doe", "John Doe"),
"affiliation" = c("Seven Bridges Genomics", "U.S. Food and Drug Administration"),
"email" = c("example@sevenbridges.com", "example@fda.gov"),
"contribution" = I(list(c("createdBy", "curatedBy"), c("authoredBy"))),
"orcid" = c("https://orcid.org/0000-0000-0000-0000", NA),
stringsAsFactors = FALSE
)
license <- "https://creativecommons.org/licenses/by/4.0/"
provenance <- compose_provenance(
name, version, review, derived_from, obsolete_after,
embargo, created, modified, contributors, license
)
provenance %>% convert_json(){
"name": "HCV1a ledipasvir resistance SNP detection",
"version": "1.0.0",
"review": [
{
"status": "approved",
"reviewer_comment": "Approved by [company name] staff. Waiting for approval from FDA Reviewer",
"date": 1510507848,
"reviewer": [
{
"reviewer_name": "Jane Doe",
"reviewer_affiliation": "Seven Bridges Genomics",
"reviewer_email": "example@sevenbridges.com",
"reviewer_contribution": "curatedBy",
"reviewer_orcid": "https://orcid.org/0000-0000-0000-0000"
}
]
},
{
"status": "approved",
"reviewer_comment": "The revised BCO looks fine",
"date": 1513110648,
"reviewer": [
{
"reviewer_name": "John Doe",
"reviewer_affiliation": "U.S. Food and Drug Administration",
"reviewer_email": "example@fda.gov",
"reviewer_contribution": "curatedBy",
"reviewer_orcid": "NA"
}
]
}
],
"derived_from": "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json",
"obsolete_after": "2018-11-12T12:30:48-0500",
"embargo": ["2017-10-12T12:30:48-0500", "2017-11-12T12:30:48-0500"],
"created": "2017-01-20T09:40:17-0500",
"modified": "2019-05-10T09:40:17-0500",
"contributors": [
{
"name": "Jane Doe",
"affiliation": "Seven Bridges Genomics",
"email": "example@sevenbridges.com",
"contribution": ["createdBy", "curatedBy"],
"orcid": "https://orcid.org/0000-0000-0000-0000"
},
{
"name": "John Doe",
"affiliation": "U.S. Food and Drug Administration",
"email": "example@fda.gov",
"contribution": "authoredBy",
"orcid": "NA"
}
],
"license": "https://creativecommons.org/licenses/by/4.0/"
} text <- c(
"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"
)
usability <- compose_usability(text)
usability %>% convert_json()["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"] fhir_endpoint <- "https://fhirtest.uhn.ca/baseDstu3"
fhir_version <- "3"
fhir_resources <- data.frame(
"id" = c("21376", "6288583", "25544", "92440", "4588936"),
"resource" = c(
"Sequence", "DiagnosticReport", "ProcedureRequest",
"Observation", "FamilyMemberHistory"
),
stringsAsFactors = FALSE
)
fhir <- compose_fhir(fhir_endpoint, fhir_version, fhir_resources)
fhir %>% convert_json(){
"fhir_endpoint": "https://fhirtest.uhn.ca/baseDstu3",
"fhir_version": "3",
"fhir_resources": [
[
{
"fhir_id": "21376",
"fhir_resource": "Sequence"
}
],
[
{
"fhir_id": "6288583",
"fhir_resource": "DiagnosticReport"
}
],
[
{
"fhir_id": "25544",
"fhir_resource": "ProcedureRequest"
}
],
[
{
"fhir_id": "92440",
"fhir_resource": "Observation"
}
],
[
{
"fhir_id": "4588936",
"fhir_resource": "FamilyMemberHistory"
}
]
]
} 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"
scm <- compose_scm(scm_repository, scm_type, scm_commit, scm_path, scm_preview)
scm %>% convert_json(){
"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"
} extension <- compose_extension(fhir, scm)
extension %>% convert_json(){
"fhir_extension": {
"fhir_endpoint": "https://fhirtest.uhn.ca/baseDstu3",
"fhir_version": "3",
"fhir_resources": [
[
{
"fhir_id": "21376",
"fhir_resource": "Sequence"
}
],
[
{
"fhir_id": "6288583",
"fhir_resource": "DiagnosticReport"
}
],
[
{
"fhir_id": "25544",
"fhir_resource": "ProcedureRequest"
}
],
[
{
"fhir_id": "92440",
"fhir_resource": "Observation"
}
],
[
{
"fhir_id": "4588936",
"fhir_resource": "FamilyMemberHistory"
}
]
]
},
"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"
}
} keywords <- c("HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions")
xref <- data.frame(
"namespace" = c("pubchem.compound", "pubmed", "so", "taxonomy"),
"name" = c("PubChem-compound", "PubMed", "Sequence Ontology", "Taxonomy"),
"ids" = I(list(
"67505836",
"26508693",
c("SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"),
"31646"
)),
"access_time" = c(
as.POSIXct("2017-01-20T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-21T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-22T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-23T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
stringsAsFactors = FALSE
)
platform <- "Seven Bridges Platform"
pipeline_meta <- data.frame(
"step_number" = c("1"),
"name" = c("HIVE-hexagon"),
"description" = c("Alignment of reads to a set of references"),
"version" = c("1.3"),
stringsAsFactors = FALSE
)
pipeline_prerequisite <- data.frame(
"step_number" = rep("1", 5),
"name" = c(
"Hepatitis C virus genotype 1",
"Hepatitis C virus type 1b complete genome",
"Hepatitis C virus (isolate JFH-1) genomic RNA",
"Hepatitis C virus clone J8CF, complete genome",
"Hepatitis C virus S52 polyprotein gene"
),
"uri" = c(
"https://www.ncbi.nlm.nih.gov/nuccore/22129792",
"https://www.ncbi.nlm.nih.gov/nuccore/5420376",
"https://www.ncbi.nlm.nih.gov/nuccore/13122261",
"https://www.ncbi.nlm.nih.gov/nuccore/386646758",
"https://www.ncbi.nlm.nih.gov/nuccore/295311559"
),
"access_time" = c(
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
stringsAsFactors = FALSE
)
pipeline_input <- data.frame(
"step_number" = rep("1", 2),
"uri" = c(
"https://example.com/dna.cgi?cmd=objFile&ids=514683",
"https://example.com/dna.cgi?cmd=objFile&ids=514682"
),
"access_time" = c(
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
stringsAsFactors = FALSE
)
pipeline_output <- data.frame(
"step_number" = rep("1", 2),
"uri" = c(
"https://example.com/data/514769/allCount-aligned.csv",
"https://example.com/data/514801/SNPProfile*.csv"
),
"access_time" = c(
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
stringsAsFactors = FALSE
)
description <- compose_description(
keywords, xref, platform,
pipeline_meta, pipeline_prerequisite, pipeline_input, pipeline_output
)
description %>% convert_json(){
"keywords": ["HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions"],
"xref": [
{
"namespace": "pubchem.compound",
"name": "PubChem-compound",
"ids": "67505836",
"access_time": "2017-01-20T09:40:17-0500"
},
{
"namespace": "pubmed",
"name": "PubMed",
"ids": "26508693",
"access_time": "2017-01-21T09:40:17-0500"
},
{
"namespace": "so",
"name": "Sequence Ontology",
"ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"],
"access_time": "2017-01-22T09:40:17-0500"
},
{
"namespace": "taxonomy",
"name": "Taxonomy",
"ids": "31646",
"access_time": "2017-01-23T09:40:17-0500"
}
],
"platform": [
"Seven Bridges Platform"
],
"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": "https://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus type 1b complete genome",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/13122261",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus clone J8CF, complete genome",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus S52 polyprotein gene",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24 09:40:17"
}
}
],
"input_list": [
{
"uri": "https://example.com/dna.cgi?cmd=objFile&ids=514683",
"access_time": "2017-01-24 09:40:17"
},
{
"uri": "https://example.com/dna.cgi?cmd=objFile&ids=514682",
"access_time": "2017-01-24 09:40:17"
}
],
"output_list": [
{
"uri": "https://example.com/data/514769/allCount-aligned.csv",
"access_time": "2017-01-24 09:40:17"
},
{
"uri": "https://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24 09:40:17"
}
]
}
]
} script <- "https://example.com/workflows/antiviral_resistance_detection_hive.py"
script_driver <- "shell"
software_prerequisites <- data.frame(
"name" = c("HIVE-hexagon", "HIVE-heptagon"),
"version" = c("babajanian.1", "albinoni.2"),
"uri" = c(
"https://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"https://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-"
),
"access_time" = c(
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
"sha1_chksum" = c("d60f506cddac09e9e816531e7905ca1ca6641e3c", NA),
stringsAsFactors = FALSE
)
external_data_endpoints <- data.frame(
"name" = c("generic name", "access to ftp server", "access to e-utils web service"),
"url" = c(
"protocol://domain:port/application/path",
"ftp://data.example.com:21/",
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
),
stringsAsFactors = FALSE
)
environment_variables <- data.frame(
"key" = c("HOSTTYPE", "EDITOR"),
"value" = c("x86_64-linux", "vim")
)
execution <- compose_execution(
script, script_driver, software_prerequisites, external_data_endpoints, environment_variables
)
execution %>% convert_json(){
"script": [
"https://example.com/workflows/antiviral_resistance_detection_hive.py"
],
"script_driver": "shell",
"software_prerequisites": [
{
"name": "HIVE-hexagon",
"version": "babajanian.1",
"uri": [
{
"uri": "https://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"access_time": "2017-01-24 09:40:17",
"sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c"
}
]
},
{
"name": "HIVE-heptagon",
"version": "albinoni.2",
"uri": [
{
"uri": "https://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-",
"access_time": "2017-01-24 09:40:17",
"sha1_chksum": "NA"
}
]
}
],
"external_data_endpoints": [
[
{
"name": "generic name",
"url": "protocol://domain:port/application/path"
}
],
[
{
"name": "access to ftp server",
"url": "ftp://data.example.com:21/"
}
],
[
{
"name": "access to e-utils web service",
"url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
}
]
],
"environment_variables": {
"HOSTTYPE": "x86_64-linux",
"EDITOR": "vim"
}
} df_parametric <- data.frame(
"param" = c(
"seed", "minimum_match_len",
"divergence_threshold_percent",
"minimum_coverage", "freq_cutoff"
),
"value" = c("14", "66", "0.30", "15", "0.10"),
"step" = c(1, 1, 1, 2, 2),
stringsAsFactors = FALSE
)
parametric <- compose_parametric(df_parametric)
parametric %>% convert_json()[
{
"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"
}
] input_subdomain <- data.frame(
"filename" = c(
"Hepatitis C virus genotype 1",
"Hepatitis C virus type 1b complete genome"
),
"uri" = c(
"https://www.ncbi.nlm.nih.gov/nuccore/22129792",
"https://www.ncbi.nlm.nih.gov/nuccore/5420376"
),
"access_time" = c(
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
stringsAsFactors = FALSE
)
output_subdomain <- data.frame(
"mediatype" = c("text/csv", "text/csv"),
"uri" = c(
"https://example.com/data/514769/dnaAccessionBased.csv",
"https://example.com/data/514801/SNPProfile*.csv"
),
"access_time" = c(
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"),
as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST")
),
stringsAsFactors = FALSE
)
io <- compose_io(input_subdomain, output_subdomain)
io %>% convert_json(){
"input_subdomain": [
{
"uri": [
{
"filename": "Hepatitis C virus genotype 1",
"uri": "https://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": "https://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
]
}
],
"output_subdomain": [
{
"mediatype": "text/csv",
"uri": [
{
"uri": "https://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
},
{
"mediatype": "text/csv",
"uri": [
{
"uri": "https://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
}
]
} empirical <- data.frame(
"key" = c("false_negative_alignment_hits", "false_discovery"),
"value" = c("<0.0010", "<0.05"),
stringsAsFactors = FALSE
)
algorithmic <- data.frame(
"key" = c("false_positive_mutation_calls", "false_discovery"),
"value" = c("<0.00005", "0.005"),
stringsAsFactors = FALSE
)
error <- compose_error(empirical, algorithmic)
error %>% convert_json(){
"empirical_error": {
"false_negative_alignment_hits": "<0.0010",
"false_discovery": "<0.05"
},
"algorithmic_error": {
"false_positive_mutation_calls": "<0.00005",
"false_discovery": "0.005"
}
} tlf <- compose_tlf(
provenance, usability, extension, description,
execution, parametric, io, error
)
tlf %>% convert_json()["https://w3id.org/biocompute/1.4.2/", "https://biocompute.sbgenomics.com/bco/44506efe-dd6f-4e4d-9444-164bdee96a7f", "d18deb41a97a3108e743231af5fec0055dac321b945a569ca58bf33503ec526b"] bco <- biocompute::compose(
tlf, provenance, usability, extension, description,
execution, parametric, io, error
)
bco %>% convert_json(){
"spec_version": "https://w3id.org/biocompute/1.4.2/",
"object_id": "https://biocompute.sbgenomics.com/bco/44506efe-dd6f-4e4d-9444-164bdee96a7f",
"etag": "d18deb41a97a3108e743231af5fec0055dac321b945a569ca58bf33503ec526b",
"provenance_domain": {
"name": "HCV1a ledipasvir resistance SNP detection",
"version": "1.0.0",
"review": [
{
"status": "approved",
"reviewer_comment": "Approved by [company name] staff. Waiting for approval from FDA Reviewer",
"date": 1510507848,
"reviewer": [
{
"reviewer_name": "Jane Doe",
"reviewer_affiliation": "Seven Bridges Genomics",
"reviewer_email": "example@sevenbridges.com",
"reviewer_contribution": "curatedBy",
"reviewer_orcid": "https://orcid.org/0000-0000-0000-0000"
}
]
},
{
"status": "approved",
"reviewer_comment": "The revised BCO looks fine",
"date": 1513110648,
"reviewer": [
{
"reviewer_name": "John Doe",
"reviewer_affiliation": "U.S. Food and Drug Administration",
"reviewer_email": "example@fda.gov",
"reviewer_contribution": "curatedBy",
"reviewer_orcid": "NA"
}
]
}
],
"derived_from": "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json",
"obsolete_after": "2018-11-12T12:30:48-0500",
"embargo": ["2017-10-12T12:30:48-0500", "2017-11-12T12:30:48-0500"],
"created": "2017-01-20T09:40:17-0500",
"modified": "2019-05-10T09:40:17-0500",
"contributors": [
{
"name": "Jane Doe",
"affiliation": "Seven Bridges Genomics",
"email": "example@sevenbridges.com",
"contribution": ["createdBy", "curatedBy"],
"orcid": "https://orcid.org/0000-0000-0000-0000"
},
{
"name": "John Doe",
"affiliation": "U.S. Food and Drug Administration",
"email": "example@fda.gov",
"contribution": "authoredBy",
"orcid": "NA"
}
],
"license": "https://creativecommons.org/licenses/by/4.0/"
},
"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"],
"extension_domain": {
"fhir_extension": {
"fhir_endpoint": "https://fhirtest.uhn.ca/baseDstu3",
"fhir_version": "3",
"fhir_resources": [
[
{
"fhir_id": "21376",
"fhir_resource": "Sequence"
}
],
[
{
"fhir_id": "6288583",
"fhir_resource": "DiagnosticReport"
}
],
[
{
"fhir_id": "25544",
"fhir_resource": "ProcedureRequest"
}
],
[
{
"fhir_id": "92440",
"fhir_resource": "Observation"
}
],
[
{
"fhir_id": "4588936",
"fhir_resource": "FamilyMemberHistory"
}
]
]
},
"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": "2017-01-20T09:40:17-0500"
},
{
"namespace": "pubmed",
"name": "PubMed",
"ids": "26508693",
"access_time": "2017-01-21T09:40:17-0500"
},
{
"namespace": "so",
"name": "Sequence Ontology",
"ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"],
"access_time": "2017-01-22T09:40:17-0500"
},
{
"namespace": "taxonomy",
"name": "Taxonomy",
"ids": "31646",
"access_time": "2017-01-23T09:40:17-0500"
}
],
"platform": [
"Seven Bridges Platform"
],
"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": "https://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus type 1b complete genome",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/13122261",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus clone J8CF, complete genome",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24 09:40:17"
}
},
{
"name": "Hepatitis C virus S52 polyprotein gene",
"uri": {
"uri": "https://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24 09:40:17"
}
}
],
"input_list": [
{
"uri": "https://example.com/dna.cgi?cmd=objFile&ids=514683",
"access_time": "2017-01-24 09:40:17"
},
{
"uri": "https://example.com/dna.cgi?cmd=objFile&ids=514682",
"access_time": "2017-01-24 09:40:17"
}
],
"output_list": [
{
"uri": "https://example.com/data/514769/allCount-aligned.csv",
"access_time": "2017-01-24 09:40:17"
},
{
"uri": "https://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24 09:40:17"
}
]
}
]
},
"execution_domain": {
"script": [
"https://example.com/workflows/antiviral_resistance_detection_hive.py"
],
"script_driver": "shell",
"software_prerequisites": [
{
"name": "HIVE-hexagon",
"version": "babajanian.1",
"uri": [
{
"uri": "https://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"access_time": "2017-01-24 09:40:17",
"sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c"
}
]
},
{
"name": "HIVE-heptagon",
"version": "albinoni.2",
"uri": [
{
"uri": "https://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-",
"access_time": "2017-01-24 09:40:17",
"sha1_chksum": "NA"
}
]
}
],
"external_data_endpoints": [
[
{
"name": "generic name",
"url": "protocol://domain:port/application/path"
}
],
[
{
"name": "access to ftp server",
"url": "ftp://data.example.com:21/"
}
],
[
{
"name": "access to e-utils web service",
"url": "https://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": "https://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": "https://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
]
}
],
"output_subdomain": [
{
"mediatype": "text/csv",
"uri": [
{
"uri": "https://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
},
{
"mediatype": "text/csv",
"uri": [
{
"uri": "https://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": "<0.00005",
"false_discovery": "0.005"
}
}
} These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.