{
    "object_id": "https://biocomputeobject.org/GLY_001203/v-2.9.1",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Bovine Protein Reactions (Reactome)",
        "version": "v-2.9.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "email": "jeetvora@gwu.edu",
                "contribution": [
                    "createdBy"
                ]
            },
            {
                "name": "Karina Martinez",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "karinamartinez@gwu.edu"
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Jingyue Wu",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jingyue.wu@email.gwu.edu"
            },
            {
                "name": "Kate Warner",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "k.warner1@gwu.edu"
            }
        ],
        "modified": "2024-10-31T16:56:03.637Z"
    },
    "usability_domain": [
        "The Bovine Protein Reactions (Reactome) dataset contains reactions information for pathways for Bos taurus [taxid:9913] UniProtKB accessions that includes reaction participants, pathway ID, reaction ID, PMID etc from Reactome database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen."
    ],
    "description_domain": {
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "step_number": 1,
                "description": "The script loads the Reactome reaction data from the triplestore containing triples from nt file to retrieve the information associated with the Reactome IDs and maps it to the UniProtKB canonical accessions and extracts the dataset in the csv format",
                "input_list": [],
                "prerequisite": [],
                "output_list": []
            }
        ],
        "keywords": [
            "Reactome",
            "Pathway",
            "Reactions",
            "PMID"
        ]
    },
    "parametric_domain": [
        {
            "value": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/bovine_protein_reactions_reactome.csv",
                    "filename": "bovine_protein_reactions_reactome.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/bovine_protein_reactions_reactome.stat.csv",
                    "filename": "bovine_protein_reactions_reactome.stat.csv"
                }
            }
        ],
        "input_subdomain": [
            {
                "uri": {
                    "filename": "all_blacklisted_pmids.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.9.1/compiled/all_blacklisted_pmids.csv"
                }
            },
            {
                "uri": {
                    "filename": "uniprot-proteome-bos-taurus.nt",
                    "uri": "https:/data.glygen.org/ln2downloads/ebi/2025_05_20/uniprot-proteome-bos-taurus.nt"
                }
            }
        ]
    },
    "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": [
        {
            "dataset_extension": {
                "dataset_categories": [
                    {
                        "category_value": "Bos taurus",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Protein",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Reactions Reactome",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ],
                "additional_license": {
                    "data_license": "https://creativecommons.org/licenses/by/4.0/",
                    "script_license": "https://www.gnu.org/licenses/gpl-3.0.en.html"
                }
            },
            "extension_schema": "https://www.w3id.org/biocompute/extension_domain/1.2.0/dataset/dataset_extension.json"
        }
    ],
    "error_domain": {},
    "etag": "711dd9d7062f55133e71534876aecdef"
}