{
    "bcoid": "GLY_000253",
    "title": "Rat Protein Citations (UniProtKB)",
    "description": "The Rat Protein Citations dataset contains publication information for Rattus norvegicus [taxid:10116] ...",
    "filename_list": "rat_protein_citations_uniprotkb.csv",
    "filename": "rat_protein_citations_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Rattus norvegicus"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Protein Citations"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "citations"
        ]
    },
    "minitable": {
        "content": [
            [
                "P05554-1...",
                "Sumoylation ..."
            ],
            [
                "P05554-1...",
                "Repression o..."
            ]
        ],
        "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"
                }
            ],
            [
                "P05554-1",
                "Sumoylation of CCAAT/enhancer-binding protein alpha and its functional roles in hepatocyte differentiation.",
                "The Journal of biological chemistry",
                "2006 Aug 4",
                "Sato Y, Miyake K, Kaneoka H, Iijima S",
                "protein_xref_pubmed",
                "16735515",
                "protein_xref_uniprotkb",
                "P05554"
            ],
            [
                "P05554-1",
                "Repression of transcriptional activity of C/EBPalpha by E2F-dimerization partner complexes.",
                "Molecular and cellular biology",
                "2010 May",
                "Zaragoza K, Begay V, Schuetz A, Heinemann U, Leutz A",
                "protein_xref_pubmed",
                "20176812",
                "protein_xref_uniprotkb",
                "P05554"
            ]
        ]
    },
    "readme": "Name\n   - Rat Protein Citations (UniProtKB)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2019-09-06T14:06:38.980261\n\nModified on\n   - 2024-05-17T11:23:53.776Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@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 Rat Protein Citations dataset contains publication information for Rattus norvegicus [taxid:10116] 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: rat_protein_blacklisted_pmids_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv\n      Name: rat_protein_function_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_function_uniprotkb.csv\n      Name: rat_protein_ptm_annotation_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_ptm_annotation_uniprotkb.csv\n      Name: rat_protein_site_annotation_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_site_annotation_uniprotkb.csv\n      Name: uniprot-proteome-rattus-norvegicus.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-rattus-norvegicus.nt\n   Output Subdomain\n      Name: rat_protein_citations_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_citations_uniprotkb.csv\n      Name: rat_protein_citations_uniprotkb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/rat_protein_citations_uniprotkb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"8445\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/rat_protein_citations_uniprotkb.csv"
}