{
    "bcoid": "GLY_001380",
    "title": "Hamster Protein Citations (UniProtKB)",
    "description": "The Hamster Protein Citations dataset contains publication information for Cricetulus griseus [taxid:10029] ...",
    "filename_list": "hamster_protein_citations_uniprotkb.csv",
    "filename": "hamster_protein_citations_uniprotkb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Cricetulus griseus"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Protein Citations"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "citations"
        ]
    },
    "minitable": {
        "content": [
            [
                "A0A061I403-1...",
                "FICD acts bi..."
            ],
            [
                "A0A061I403-1...",
                "AMPylation t..."
            ]
        ],
        "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"
                }
            ],
            [
                "A0A061I403-1",
                "FICD acts bifunctionally to AMPylate and de-AMPylate the endoplasmic reticulum chaperone BiP.",
                "Nature structural & molecular biology",
                "2017 Jan",
                "Preissler S, Rato C, Perera L, Saudek V, Ron D",
                "protein_xref_pubmed",
                "27918543",
                "protein_xref_uniprotkb",
                "A0A061I403"
            ],
            [
                "A0A061I403-1",
                "AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation.",
                "eLife",
                "2017-10-24",
                "Preissler Steffen, Rohland Lukas, Yan Yahui, Chen Ruming, Read Randy J, Ron David",
                "protein_xref_pubmed",
                "29064368",
                "protein_xref_uniprotkb",
                "A0A061I403"
            ]
        ]
    },
    "readme": "Name\n   - Hamster Protein Citations (UniProtKB)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - \n\nModified on\n   - \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 Hamster Protein Citations dataset contains publication information for Cricetulus griseus [taxid:10029] 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: hamster_protein_function_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/hamster_protein_function_uniprotkb.csv\n      Name: hamster_protein_ptm_annotation_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/hamster_protein_ptm_annotation_uniprotkb.csv\n      Name: hamster_protein_site_annotation_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/hamster_protein_site_annotation_uniprotkb.csv\n      Name: uniprot-proteome-cricetulus-griseus.nt\n      URI: https:/data.glygen.org/ln2downloads/ebi/2026_06_13/uniprot-proteome-cricetulus-griseus.nt\n   Output Subdomain\n      Name: hamster_protein_citations_uniprotkb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/hamster_protein_citations_uniprotkb.csv\n      Name: hamster_protein_citations_uniprotkb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/hamster_protein_citations_uniprotkb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"21239\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/hamster_protein_citations_uniprotkb.csv"
}