{
    "object_id": "https://biocomputeobject.org/GLY_001126/v-2.8.1",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "GlyGen-Flybase Crossreferences Mapping",
        "version": "v-2.8.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "modified": "2024-07-24T13:28:13.683Z",
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "email": "jeetvora@gwu.edu",
                "contribution": [
                    "createdBy"
                ]
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Karina Martinez",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Luke Johnson",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "luke.johnson@email.gwu.edu"
            },
            {
                "name": "Urnisha Bhuiyan",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "sbhuiyan28@email.gwu.edu"
            },
            {
                "name": "Cyrus Au-Yeung",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "cyruschauyeung@gwu.edu"
            },
            {
                "name": "Kate Warner",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "k.warner1@gwu.edu"
            }
        ]
    },
    "usability_domain": [
        "The GlyGen-Flybase Cross-references Mapping dataset contains GlyGen's Drosophila melanogaster [taxid:7227] UniProtKB accessions cross-referenced to FlyBase database identifiers. The dataset is created for the Flybase database to crosslink their protein page links to GlyGen protein pages, and is formatted as per the 'Links from FlyBase' guidelines where the DbName is GlyGen. The *linkout.tsv is four column TSV, Column 1 - FlyBase ID, Column 2 - DBNAME, Column 3 - DBID, Column 4 - DBURL. The database information file is named glygen_dbinfo.tsv that contains five lines and can be accessed from GlyGen Sharepoint."
    ],
    "description_domain": {
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "step_number": 1,
                "input_list": [],
                "description": "The script loads the fruitfly UniProtKB GlyGen accessions, maps them to their Flybase IDs, and extracts the data into the tsv dataset file.",
                "prerequisite": [],
                "output_list": []
            }
        ],
        "keywords": [
            "crossreferences",
            "fruitfly",
            "GlyGen",
            "Flybase"
        ]
    },
    "parametric_domain": [
        {
            "value": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "tsv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/protein_glygen_flybase_linkout.tsv",
                    "filename": "protein_glygen_flybase_linkout.tsv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/protein_glygen_flybase_linkout.stat.csv",
                    "filename": "protein_glygen_flybase_linkout.stat.csv"
                }
            }
        ],
        "input_subdomain": []
    },
    "execution_domain": {
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py",
                    "filename": "make-protein-dataset.py"
                }
            }
        ],
        "script_driver": "manual",
        "software_prerequisites": [
            {
                "version": "2.7.5",
                "name": "Python",
                "uri": {
                    "uri": "https://www.python.org/download/releases/2.7.5/"
                }
            }
        ],
        "external_data_endpoints": [],
        "environment_variables": {}
    },
    "extension_domain": [
        {
            "extension_schema": "https://www.w3id.org/biocompute/extension_domain/1.2.0/dataset/dataset_extension.json",
            "dataset_extension": {
                "additional_license": {
                    "data_license": "https://creativecommons.org/licenses/by/4.0/",
                    "script_license": "https://www.gnu.org/licenses/gpl-3.0.en.html"
                },
                "dataset_categories": [
                    {
                        "category_value": "Drosophila melanogaster",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Protein",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "GlyGen-Flybase Crossreferences",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "tsv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "external",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "error_domain": {},
    "etag": "b17150eaf9104efd75ab253add99ddc0"
}