{
    "bcoid": "GLY_000749",
    "title": "Yeast Protein Citations (UniProtKB)",
    "description": "The Yeast Protein Citations dataset contains publication information for Saccharomyces cerevisiae S288C ...",
    "filename_list": "yeast_protein_citations_uniprotkb.csv",
    "filename": "yeast_protein_citations_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Saccharomyces cerevisiae S288C"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Protein Citations"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "citations"
        ]
    },
    "minitable": {
        "content": [
            [
                "P20606-1...",
                "Dynamics of ..."
            ],
            [
                "P20606-1...",
                "The use of l..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "title..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "title"
                },
                {
                    "type": "string",
                    "label": "journal_name"
                },
                {
                    "type": "string",
                    "label": "publication_date"
                },
                {
                    "type": "string",
                    "label": "authors"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "src_xref_key"
                },
                {
                    "type": "string",
                    "label": "src_xref_id"
                }
            ],
            [
                "P20606-1",
                "Dynamics of the COPII coat with GTP and stable analogues.",
                "Nature cell biology",
                "2001-06",
                "Antonny B, Madden D, Hamamoto S, Orci L, Schekman R",
                "protein_xref_pubmed",
                "11389436",
                "protein_xref_uniprotkb",
                "P20606"
            ],
            [
                "P20606-1",
                "The use of liposomes to study COPII- and COPI-coated vesicle formation and membrane protein sorting.",
                "Methods (San Diego, Calif.)",
                "2000-04",
                "Matsuoka K, Schekman R",
                "protein_xref_pubmed",
                "10720463",
                "protein_xref_uniprotkb",
                "P20606"
            ]
        ]
    },
    "readme": "Name\n   - Yeast Protein Citations (UniProtKB)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2022-08-30T14:17:09.307325\n\nModified on\n   - 2025-03-04T16:56:07.108Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n   - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n   - \n\nUsability Domain\n   - The Yeast Protein Citations dataset contains publication information for Saccharomyces cerevisiae S288C [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. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen.\n\nDescription Domain\n   Keywords\n   - publications\n   - PMID\n   - journal\n   - citations\n   - authors\n   - UniProtKB\n   - PubMed\n\n   Pipeline Steps\n   - Step-1: 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.\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n   Software Prerequisites\n      Name: Python\n      Version: 2.7.5\n      URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n   Input Subdomain\n      Name: all_blacklisted_pmids.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/all_blacklisted_pmids.csv\n      Name: yeast_protein_function_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/yeast_protein_function_uniprotkb.csv\n      Name: yeast_protein_ptm_annotation_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/yeast_protein_ptm_annotation_uniprotkb.csv\n      Name: yeast_protein_site_annotation_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/yeast_protein_site_annotation_uniprotkb.csv\n      Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-saccharomyces-cerevisiae.nt\n   Output Subdomain\n      Name: yeast_protein_citations_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/yeast_protein_citations_uniprotkb.csv\n      Name: yeast_protein_citations_uniprotkb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/yeast_protein_citations_uniprotkb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"6065\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/yeast_protein_citations_uniprotkb.csv"
}