{
    "object_id": "https://biocomputeobject.org/GLY_000776/v-2.5.1",
    "etag": "10472b0c9664b4a25fde6c6bbad81e1f",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Yeast Transcript Locus (Ensembl Transcript coordinates)",
        "version": "v-2.5.1",
        "created": "2022-08-31T11:17:02.109861",
        "modified": "2024-05-17T11:24:12.801Z",
        "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"
            },
            {
                "name": "Jingyue Wu",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jingyue.wu@email.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": [
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                ],
                "email": "k.warner1@gwu.edu"
            }
        ],
        "license": "https://creativecommons.org/licenses/by/4.0/"
    },
    "usability_domain": [
        "The Yeast Transcript Locus (Ensembl Transcript coordinates)s contains UniProtKB yeast [taxid:559292] canonical accessions mapped to their isoforms with further mapping to the corresponding ENSEMBL Transcript ID, Peptide ID, chromosome ID along with the transcripts' start and end position. 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": {
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                    "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": "Saccharomyces cerevisiae S288C",
                        "category_name": "species"
                    },
                    {
                        "category_value": "Protein",
                        "category_name": "molecule"
                    },
                    {
                        "category_value": "Transcript Coordinates",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
                    },
                    {
                        "category_value": "internal",
                        "category_name": "scope"
                    }
                ]
            }
        }
    ],
    "description_domain": {
        "keywords": [
            "transcript locus",
            "ensembl transcript id",
            "ensembl peptide id",
            "chromosome",
            "Ensembl"
        ],
        "pipeline_steps": [
            {
                "step_number": 1,
                "name": "make-protein-dataset.py",
                "description": "The script loads the UniProtKB accessions that are mapped to UniProtKB isoforms and ENSEMBL Transcript and Peptide identifiers from the triplestore containing triples from nt file and maps it to the UniProtKB canonical accession to finally extract the data as a csv dataset. ",
                "version": "",
                "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": {
        "input_subdomain": [
            {
                "uri": {
                    "filename": "uniprot-proteome-saccharomyces-cerevisiae.nt",
                    "uri": "https:/data.glygen.org/ln2downloads/ebi/2024_04_08/uniprot-proteome-saccharomyces-cerevisiae.nt"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/yeast_protein_transcriptlocus.csv",
                    "filename": "yeast_protein_transcriptlocus.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.5.1/reviewed/yeast_protein_transcriptlocus.stat.csv",
                    "filename": "yeast_protein_transcriptlocus.stat.csv"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    }
}