{
    "provenance_domain": {
        "name": "Fruitfly Protein Reactions (Reactome)",
        "version": "v-2.0.3",
        "created": "2022-09-06T11:25:28.437609",
        "modified": "2022-09-26T09:08:12.647223",
        "contributors": [
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Jeet Vora",
                "email": "jeetvora@gwu.edu"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Robel Kahsay",
                "email": "rykahsay@gwu.edu"
            },
            {
                "affiliation": "EMBL-EBI-UniProt",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Maria Martin",
                "email": "martin@ebi.ac.uk"
            },
            {
                "affiliation": "EMBL-EBI-UniProt",
                "contribution": [
                    "contributedBy"
                ],
                "name": "Preethi Vasudev",
                "email": "pvasudev@ebi.ac.uk"
            },
            {
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "name": "Karina Martinez",
                "email": "karinamartinez@gwu.edu"
            }
        ],
        "license": "https://creativecommons.org/licenses/by/4.0/"
    },
    "usability_domain": [
        "The Fruitfly Protein Reactions (Reactome) dataset contains reactions information for pathways for fruitfly [taxid:7227] 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, Reactome and GlyGen"
    ],
    "extension_domain": [
        {
            "extension_schema": "http://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": "Reactions Reactome",
                        "category_name": "tags"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "description_domain": {
        "keywords": [
            "Reactome",
            "Pathway",
            "Reactions",
            "PMID"
        ],
        "pipeline_steps": [
            {
                "step_number": 1,
                "name": "make-protein-dataset.py",
                "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",
                "version": "",
                "prerequisite": [],
                "input_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-2.0.3/source/uniprot-proteome-drosophila-melanogaster.nt",
                        "filename": "uniprot-proteome-drosophila-melanogaster.nt"
                    },
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-2.0.3/reviewed/fruitfly_protein_masterlist.csv",
                        "filename": "fruitfly_protein_masterlist.csv"
                    }
                ],
                "output_list": [
                    {
                        "uri": "https://data.glygen.org/ln2data/releases/data/v-2.0.3/reviewed/fruitfly_protein_reactions_reactome.csv",
                        "filename": "fruitfly_protein_reactions_reactome.csv"
                    }
                ]
            }
        ]
    },
    "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": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "uniprot-proteome-drosophila-melanogaster.nt",
                    "uri": "/data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-drosophila-melanogaster.nt"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/fruitfly_protein_reactions_reactome.csv",
                    "filename": "fruitfly_protein_reactions_reactome.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/fruitfly_protein_reactions_reactome.stat.csv",
                    "filename": "fruitfly_protein_reactions_reactome.stat.csv"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    },
    "object_id": "https://biocomputeobject.org/GLY_000686/v-2.0.3",
    "spec_version": "1.3.0",
    "etag": "a89dadfee873206d20f7c8c0b7ffa0db"
}