{
    "object_id": "https://biocomputeobject.org/GLY_000749/v-2.3.1",
    "etag": "327ae3e8016ad257448f6610b5c55101",
    "spec_version": "1.3.0",
    "provenance_domain": {
        "name": "Yeast Protein Citations (UniProtKB)",
        "version": "v-2.3.1",
        "created": "2022-08-30T14:17:09.307325",
        "modified": "2023-09-11T18:58:26",
        "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": "Jingyue Wu",
                "affiliation": "The George Washington University",
                "contribution": [
                    "createdBy"
                ],
                "email": "jingyue.wu@email.gwu.edu"
            }
        ],
        "license": "https://creativecommons.org/licenses/by/4.0/"
    },
    "usability_domain": [
        "The Yeast Protein Citations dataset contains publication information for yeast [taxid:559292] UniProtKB accessions that includes PMID, journal name, date and author and title. Publications of large scale studies, and high frequency publications pertaining to genome sequencing, cDNA, chromosomes have been filtered out as per https://data.glygen.org/ln2data/releases/data/v-1.12.3/compiled/yeast_protein_blacklisted_pmids_uniprotkb.csv. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen"
    ],
    "extension_domain": [
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                    "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": "Protein Citations",
                        "category_name": "tag"
                    },
                    {
                        "category_value": "csv",
                        "category_name": "file_type"
                    },
                    {
                        "category_value": "Reviewed",
                        "category_name": "status"
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                        "category_value": "internal",
                        "category_name": "scope"
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            }
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            "journal",
            "citations",
            "authors",
            "UniProtKB",
            "PubMed"
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        "pipeline_steps": [
            {
                "step_number": 1,
                "name": "make-protein-dataset.py",
                "description": "The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file.",
                "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",
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                }
            }
        ],
        "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/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt"
                }
            }
        ],
        "output_subdomain": [
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_protein_citations_uniprotkb.csv",
                    "filename": "yeast_protein_citations_uniprotkb.csv"
                }
            },
            {
                "mediatype": "csv",
                "uri": {
                    "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_protein_citations_uniprotkb.stat.csv",
                    "filename": "yeast_protein_citations_uniprotkb.stat.csv"
                }
            }
        ]
    },
    "error_domain": {
        "empirical_error": {},
        "algorithmic_error": {}
    }
}