{
    "object_id": "https://biocomputeobject.org/GLY_001309/v-2.12.1",
    "etag": "d5f27f7327bc3496c9b15d77cf244a41",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Zebrafish Reactions Rhea",
        "version": "v-2.12.1",
        "license": "https://creativecommons.org/licenses/by/4.0/",
        "created": "",
        "modified": "",
        "contributors": [
            {
                "name": "",
                "affiliation": "",
                "contribution": [
                    "createdBy"
                ],
                "email": "jeetvora@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 (Rhea) dataset contains reactions information for pathways for Danio rerio [taxid:7955] UniProtKB accessions that includes reaction participants ID, reaction ID, pathway ID, summary etc from Rhea database. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB, Rhea 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 Rhea",
                        "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": [
            "Rhea",
            "Reactions",
            "Participants",
            "Enzymes"
        ],
        "pipeline_steps": [
            {
                "name": "make-protein-dataset.py",
                "version": "",
                "step_number": 1,
                "description": "The script loads the Rhea reaction data from the triplestore containing triples from nt file to retrieve the information associated with the Rhea reaction IDs and maps it to the UniProtKB canonical accessions and extracts the dataset in the csv format",
                "prerequisite": [],
                "input_list": [],
                "output_list": []
            }
        ]
    },
    "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": {}
    },
    "parametric_domain": [
        {
            "param": "",
            "value": "",
            "step": ""
        }
    ],
    "io_domain": {
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/zebrafish_protein_reactions_rhea.csv",
                    "filename": "zebrafish_protein_reactions_rhea.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/zebrafish_protein_reactions_rhea.stat.csv",
                    "filename": "zebrafish_protein_reactions_rhea.stat.csv"
                }
            }
        ],
        "input_subdomain": [
            {
                "uri": {
                    "filename": "uniprot-proteome-danio-rerio.nt",
                    "uri": "https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-danio-rerio.nt"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    }
}