{
    "object_id": "https://biocomputeobject.org/GLY_001308/v-2.12.1",
    "etag": "6565538f3f095b4fb6b95e9c9efe43c7",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Zebrafish Protein Reactions (Reactome)",
        "version": "v-2.12.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "created": "",
        "modified": "",
        "contributors": [
            {
                "name": "Jeet Vora",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jeetvora@gwu.edu"
            },
            {
                "name": "Robel Kahsay",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "rykahsay@gwu.edu"
            },
            {
                "name": "Maria Martin",
                "affiliation": "EMBL-EBI-UniProt",
                "contribution": [
                    "contributedBy"
                ],
                "email": "martin@ebi.ac.uk"
            },
            {
                "name": "Preethi Vasudev",
                "affiliation": "EMBL-EBI-UniProt",
                "contribution": [
                    "contributedBy"
                ],
                "email": "pvasudev@ebi.ac.uk"
            },
            {
                "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 Zebrafish Protein Reactions (Reactome) dataset contains reactions information for pathways for Danio rerio [taxid:7955] 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."
    ],
    "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": "Danio rerio",
                        "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"
                    },
                    {
                        "category_name": "file_category",
                        "category_value": "pathway/enzymes"
                    }
                ]
            }
        }
    ],
    "description_domain": {
        "keywords": [
            "Reactome",
            "Pathway",
            "Reactions",
            "PMID"
        ],
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "step_number": 1,
                "input_list": [],
                "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",
                "prerequisite": [],
                "output_list": []
            }
        ]
    },
    "execution_domain": {
        "external_data_endpoints": [],
        "environment_variables": {},
        "script_driver": "manual",
        "software_prerequisites": [
            {
                "version": "2.7.5",
                "name": "Python",
                "uri": {
                    "uri": "https://www.python.org/download/releases/2.7.5/"
                }
            }
        ],
        "script": [
            {
                "uri": {
                    "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py",
                    "filename": "make-protein-dataset.py"
                }
            }
        ]
    },
    "parametric_domain": [
        {
            "value": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/zebrafish_protein_reactions_reactome.csv",
                    "filename": "zebrafish_protein_reactions_reactome.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/zebrafish_protein_reactions_reactome.stat.csv",
                    "filename": "zebrafish_protein_reactions_reactome.stat.csv"
                }
            }
        ],
        "input_subdomain": [
            {
                "uri": {
                    "filename": "all_blacklisted_pmids.csv",
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/all_blacklisted_pmids.csv"
                }
            },
            {
                "uri": {
                    "filename": "uniprot-proteome-danio-rerio.nt",
                    "uri": "https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-danio-rerio.nt"
                }
            }
        ]
    },
    "error_domain": {}
}