Export BioCompute Object as JSON
export_json(x, file)BioCompute Object JSON string from convert_json
JSON file path
Path to the output file
file_json <- tempfile(fileext = ".json")
generate_example("HCV1a") %>%
convert_json() %>%
export_json(file_json)
cat(paste(readLines(file_json), collapse = "\n"))
#> {
#> "spec_version": "https://w3id.org/biocompute/1.4.2/",
#> "object_id": "https://biocompute.sbgenomics.com/bco/9916e5ac-b7e4-45a0-9074-d2f55ff35f9a",
#> "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"
#> }
#> }
#> }