{
    "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",
                "reviewer_comment": "Approved by GW staff. Waiting for approval from FDA Reviewer",
                "date": "2017-11-12T12:30:48-0400",
                "reviewer": {
                    "name": "Charles Hadley King",
                    "affiliation": "George Washington University",
                    "email": "hadley_king@gwu.edu",
                    "contribution": [
                        "curatedBy"
                    ],
                    "orcid": "https://orcid.org/0000-0003-1409-4549"
                }
            },
            {
                "status": "approved",
                "reviewer_comment": "The revised BCO looks fine",
                "date": "2017-12-12T12:30:48-0400",
                "reviewer": {
                    "name": "Eric Donaldson",
                    "affiliation": "FDA",
                    "email": "Eric.Donaldson@fda.hhs.gov",
                    "contribution": [
                        "curatedBy"
                    ]
                }
            }
        ],
        "obsolete_after": "2118-09-26T14:43:43-0400",
        "embargo": {
            "start_time": "2000-09-26T14:43:43-0400",
            "end_time": "2000-09-26T14:43:45-0400"
        },
        "created": "2017-01-24T09:40:17-0500",
        "modified": "2018-09-21T14:06:14-0400",
        "contributors": [
            {
                "name": "Charles Hadley King",
                "affiliation": "George Washington University",
                "email": "hadley_king@gwu.edu",
                "contribution": [
                    "createdBy",
                    "curatedBy"
                ],
                "orcid": "https://orcid.org/0000-0003-1409-4549"
            },
            {
                "name": "Eric Donaldson",
                "affiliation": "FDA",
                "email": "Eric.Donaldson@fda.hhs.gov",
                "contribution": [
                    "authoredBy"
                ]
            }
        ],
        "license": "https://spdx.org/licenses/CC-BY-4.0.html"
    },
    "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",
        "GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
    ],
    "extension_domain": [
        {
            "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/fhir/fhir_extension.json",
            "fhir_extension": [
                {
                    "fhir_endpoint": "http://fhirtest.uhn.ca/baseDstu3",
                    "fhir_version": "3",
                    "fhir_resources": [
                        {
                            "fhir_resource": "Sequence",
                            "fhir_id": "21376"
                        },
                        {
                            "fhir_resource": "DiagnosticReport",
                            "fhir_id": "6288583"
                        },
                        {
                            "fhir_resource": "ProcedureRequest",
                            "fhir_id": "25544"
                        },
                        {
                            "fhir_resource": "Observation",
                            "fhir_id": "92440"
                        },
                        {
                            "fhir_resource": "FamilyMemberHistory",
                            "fhir_id": "4588936"
                        }
                    ]
                }
            ]
        }, 
        {
            "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json",
            "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": "2018-13-02T10:15-05:00"
            },
            {
                "namespace": "pubmed",
                "name": "PubMed",
                "ids": [
                    "26508693"
                ],
                "access_time": "2018-13-02T10:15-05:00"
            },
            {
                "namespace": "so",
                "name": "Sequence Ontology",
                "ids": [
                    "SO:0000002",
                    "SO:0000694",
                    "SO:0000667",
                    "SO:0000045"
                ],
                "access_time": "2018-13-02T10:15-05:00"
            },
            {
                "namespace": "taxonomy",
                "name": "Taxonomy",
                "ids": [
                    "31646"
                ],
                "access_time": "2018-13-02T10:15-05:00"
            }
        ],
        "platform": [
            "HIVE"
        ],
        "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": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
                            "access_time": "2017-01-24T09:40:17-0500"
                        }
                    },
                    {
                        "name": "Hepatitis C virus type 1b complete genome",
                        "uri": {
                            "uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
                            "access_time": "2017-01-24T09:40:17-0500"
                        }
                    },
                    {
                        "name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
                        "uri": {
                            "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": [
                    {
                        "uri": "http://example.com/data/514769/allCount-aligned.csv",
                        "access_time": "2017-01-24T09:40:17-0500"
                    }
                ]
            },
            {
                "step_number": 2,
                "name": "HIVE-heptagon",
                "description": "variant calling",
                "version": "1.3",
                "input_list": [
                    {
                        "uri": "http://example.com/data/514769/dnaAccessionBased.csv",
                        "access_time": "2017-01-24T09:40:17-0500"
                    }
                ],
                "output_list": [
                    {
                        "uri": "http://example.com/data/514801/SNPProfile.csv",
                        "access_time": "2017-01-24T09:40:17-0500"
                    },
                    {
                        "uri": "http://example.com/data/14769/allCount-aligned.csv",
                        "access_time": "2017-01-24T09:40:17-0500"
                    }
                ]
            }
        ]
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://example.com/workflows/antiviral_resistance_detection_hive.py"
                }
            }
        ],
        "script_driver": "shell",
        "software_prerequisites": [
            {
                "name": "HIVE-hexagon",
                "version": "babajanian.1",
                "uri": {
                    "uri": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
                    "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"
                }
            },
            {
                "uri": {
                    "uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
                    "access_time": "2017-01-24T09:40:17-0500"
                }
            },
            {
                "uri": {
                    "filename": "Hepatitis C virus S52 polyprotein gene",
                    "uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
                    "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": {
            "false_negative_alignment_hits": "<0.0010",
            "false_discovery": "<0.05"
        },
        "algorithmic_error": {
            "false_positive_mutation_calls_discovery": "<0.00005",
            "false_discovery": "0.005"
        }
    }
}