{
    "object_id": "https://raw.githubusercontent.com/biocompute-objects/BCO_Specification/1.4.2/examples/HIVE_metagenomics.json",
    "etag": "caed07395b6afb58c8810d174a315260124f687740bc3bb14387de5e84c7e3d4",
    "spec_version" : "https://w3id.org/ieee/ieee-2791-schema/",
    "provenance_domain": {
        "name": "Healthy human fecal metagenomic diversity", 
        "version": "1.0.0",
        "review": [
            {
                "status": "approved",
                "reviewer_comment": "Approved by GW staff.",
                "reviewer": {
                    "name": "Charles Hadley King", 
                    "affiliation": "George Washington University", 
                    "email": "hadley_king@gwu.edu",
                    "contribution": ["curatedBy"],
                    "orcid": "https://orcid.org/0000-0003-1409-4549"
                }
            }
        ],
        "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": "2018-11-29T11:29:08-0500", 
        "modified": "2018-11-30T11:29:08-0500", 
        "contributors": [
            {
                "name": "Charles Hadley King", 
                "affiliation": "George Washington University", 
                "email": "hadley_king@gwu.edu",
                "contribution": ["createdBy", "curatedBy", "authoredBy"],
                "orcid": "https://orcid.org/0000-0003-1409-4549"
            },
            {
                "name": "Raja Mazumder", 
                "affiliation": "George Washington University", 
                "email": "mazumder@gwu.edu",
                "contribution": ["createdBy", "curatedBy", "authoredBy"],
                "orcid": "https://orcid.org/0000-0001-88238-9945"
            }
        ],
        "license": "https://spdx.org/licenses/CC-BY-4.0.html"
    },
    "usability_domain": [
        "Identify the most common organism present in a human [taxID:9606] fecal [UBERON:0001988] sample, ", 
        "Identify the general community composition of organisms in a human [taxID:9606] fecal [UBERON:0001988] sample, ", 
        "CensuScope is used to do a census of the composition of the read files. Based on a user-defined threshold, organisms identified are used for alignment in the Hexagon alignment."
    ],
    "extension_domain":[
        {
            "extension_schema": "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm/scm_extension.json",
            "scm_extension": {
                "scm_repository": "https://github.com/biocompute-objects/HIVE_metagenomics",
                "scm_type": "git",
                "scm_commit": "e4620f642fb20557f6c679397696614305ed07b1",
                "scm_path": "biocompute-objects/HIVE_metagenomics",
                "scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
                }
        }
    ],
    "description_domain": {
        "keywords": [
            "metagenome", 
            "metagenomic analysis", 
            "fecal"
        ], 
        "xref": [
            {
                "namespace": "uberon",
                "name": "Uber Anatomy Ontology",
                "ids": ["0001988"], 
                "access_time": "2016-11-30T06:46-0500"
            },
            {
                "namespace": "taxonomy",
                "name": "Taxonomy",
                "ids": ["9606"], 
                "access_time": "2016-11-30T06:46-0500"
            }
        ], 
        "platform": ["hive"], 
        "pipeline_steps": [
            {
                "step_number": 1,
                "name": "CensuScope", 
                "description": "Detect taxonomic composition of a metagenomic data set.", 
                "version": "1.3", 
                "prerequisite": [
                    {
                        "name": "Filtered_NT_feb18_2016", 
                        "uri": {
                            "uri": "https://hive.biochemistry.gwu.edu/genome/513957",
                            "access_time": "2016-11-30T06:46-0500"
                        }
                    }
                ],
                "input_list": [
                    {
                        "uri": "https://hive.biochemistry.gwu.edu/nuc-read/545722",
                        "access_time": "2016-11-30T06:46-0500"
                    }, 
                    {
                        "uri": "https://hive.biochemistry.gwu.edu/nuc-read/545721",
                        "access_time": "2016-11-30T06:46-0500"
                    }
                ], 
                "output_list": [
                    {
                        "uri": "https://hive.biochemistry.gwu.edu/546223/dnaAccessionBasedResult.csv",
                        "access_time": "2016-11-30T06:46-0500"
                    }
                ]
            },
            {
                "step_number": 2, 
                "name": "HIVE-hexagon", 
                "description": "Alignment of reads to a set of references", 
                "version": "1.3", 
                "input_list": [
                    {
                        "uri": "http://example.com/data/546223/dnaAccessionBased.csv",
                        "access_time": "2016-11-30T06:46-0500"
                    },
                    {
                        "uri": "https://hive.biochemistry.gwu.edu/nuc-read/545722",
                        "access_time": "2016-11-30T06:46-0500"
                    }, 
                    {
                        "uri": "https://hive.biochemistry.gwu.edu/nuc-read/545721",
                        "access_time": "2016-11-30T06:46-0500"
                    }
                ], 
                "output_list": [
                    {
                        "uri": "https://hive.biochemistry.gwu.edu/546232/alCount-Unalignedo524569-alCount--1.csv",
                        "access_time": "2016-11-30T06:46-0500"
                    }
                ]
            }
        ]
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/biocompute-objects/HIVE_metagenomics/blob/master/driverHIVEmetagenomic.py"
                }
            }
        ],
        "script_driver": "shell",
        "software_prerequisites": [
            {
                "name": "CensuScope", 
                "version": "albinoni.2",
                "uri": {
                    "uri": "http://example.com/dna.cgi?cmd=dna-screening&cmdMode=-",
                    "access_time": "2017-01-24T09:40:17-0500"
                }
            },
            {
                "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"
                }
            }
        ],
        "external_data_endpoints": [
            {
                "name": "HIVE", 
                "url": "https://hive.biochemistry.gwu.edu/dna.cgi?cmd=login"
            }, 
            {
                "name": "access to e-utils", 
                "url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
            }
        ], 
        "environment_variables": {
            "key": "HOSTTYPE", 
            "value" : "x86_64-linux"
        }
    }, 
    "parametric_domain": [
        {"param": "seed", "value": "14", "step": "2"},
        {"param":"minimum_match_len", "value": "66", "step": "2"},
        {"param": "divergence_threshold_percent", "value": "0.30", "step": "2"},
        {"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": {
                    "filename": "Hepatitis C virus clone J8CF, complete genome", 
                    "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"
        }
    }
}
