{
    "bcoid": "GLY_000493",
    "title": "Rat Glycosylation Sites [Automatic Literature Mining]",
    "description": "List of rat [taxid:10116] proteins with information on glycosylation sites detected from PubMed database(abstracts-only) ...",
    "filename": "rat_proteoform_glycosylation_sites_literature_mining.csv",
    "filetype": "csv",
    "categories": {
        "status": "Reviewed",
        "molecule": "Proteoform",
        "species": "Rattus norvegicus",
        "tags": "glycosylation sites",
        "file_type": "csv",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "Q8R456-1...",
                "35..."
            ],
            [
                "Q8R456-1...",
                "35..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "glycosylatio..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "glycosylation_site_uniprotkb"
                },
                {
                    "type": "string",
                    "label": "amino_acid"
                },
                {
                    "type": "string",
                    "label": "saccharide"
                },
                {
                    "type": "string",
                    "label": "glycosylation_type"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "xref_key"
                }
            ],
            [
                "Q8R456-1",
                "35",
                "Asn",
                "",
                "n-linked",
                "GLYDS000493",
                "protein_xref_glygen_ds"
            ],
            [
                "Q8R456-1",
                "35",
                "Asn",
                "",
                "n-linked",
                "19413349",
                "protein_xref_pubmed"
            ],
            [
                "P21463-1",
                "198",
                "Asn",
                "",
                "n-linked",
                "GLYDS000493",
                "protein_xref_glygen_ds"
            ],
            [
                "P21463-1",
                "198",
                "Asn",
                "",
                "n-linked",
                "19299457",
                "protein_xref_pubmed"
            ],
            [
                "Q8R456-1",
                "31",
                "Asn",
                "",
                "n-linked",
                "GLYDS000493",
                "protein_xref_glygen_ds"
            ],
            [
                "Q8R456-1",
                "31",
                "Asn",
                "",
                "n-linked",
                "19413349",
                "protein_xref_pubmed"
            ],
            [
                "P61016-1",
                "16",
                "Ser",
                "",
                "o-linked",
                "GLYDS000493",
                "protein_xref_glygen_ds"
            ],
            [
                "P61016-1",
                "16",
                "Ser",
                "",
                "o-linked",
                "20484118",
                "protein_xref_pubmed"
            ],
            [
                "P21463-1",
                "200",
                "Thr",
                "",
                "o-linked",
                "GLYDS000493",
                "protein_xref_glygen_ds"
            ],
            [
                "P21463-1",
                "200",
                "Thr",
                "",
                "o-linked",
                "19299457",
                "protein_xref_pubmed"
            ]
        ]
    },
    "readme": "Name\n   - Rat Glycosylation Sites [Automatic Literature Mining]\n\nVersion\n   - 1.5.30\n\nCreated on\n  - 2020-04-30T10:34:38.124446\n\nModified on\n   - 2020-04-30T10:37:10.107494\n\nCreated by\n   - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@email.gwu.edu]\n\nAuthors\n   - Rahi Navelkar [rsn13@gwu.edu], Vijay Shanker [vijay@udel.edu], Karen Ross [ker25@georgetown.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nChecksum\n   - \n\nUsability Domain\n   - List of rat [taxid:10116] proteins with information on glycosylation sites detected from PubMed database(abstracts-only) through Automatic mining tool developed by Dr. Vijay Shanker (University of Delaware). The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000001)\n\nDescription Domain\n   Keywords\n   - proteins\n   - canonical\n   - glycosylation sites\n   - GlyTouCan\n   - Automatic Literature Mining\n\n   Pipeline Steps\n   - Step-1: The input file was downloaded from the provider(s). Following QC steps were done using a python script: 1. Map the uniprotkb accessions to uniprotkb canonical accessions. 2. Validate the \"amino_acid\" and \"glycosylation_site\" with the .fasta sequence. 3. Add new column: Evidence with 2 values: Automatic literature Mining | GLYDS000481  (split into 2 rows)4.change column headers: uniprotkb_ac to uniprotkb_canonical_ac\n\nExecution Domain\n   Scripts   - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-proteoform-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: proteoform_glycosylation_sites_literature_mining.csv\n      URI: https://data.glygen.org/ln2wwwdata/source/proteoform_glycosylation_sites_literature_mining.csv\n   Output Subdomain\n      Name: rat_proteoform_glycosylation_sites_literature_mining.csv\n      URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv\n      Name: rat_proteoform_glycosylation_sites_literature_mining.stat.csv\n      URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_proteoform_glycosylation_sites_literature_mining.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n      Unique Values: \"3\"\n      Name: \"glycosylation_site_uniprotkb\"\n     Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n      Unique Values: \"5\"\n      Name: \"xref_id\"\n     Description: \"\"\n      Unique Values: \"4\"\n      Name: \"glycosylation_type\"\n     Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n      Unique Values: \"2\"\n      Name: \"amino_acid\"\n     Description: \"Three letter abbreviation code of the amino acid\"\n      Unique Values: \"3\"\n      Name: \"saccharide\"\n     Description: \"Sugar\"\n      Unique Values: \"1\"\n      Name: \"xref_key\"\n     Description: \"\"\n      Unique Values: \"2\"",
    "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/rat_proteoform_glycosylation_sites_literature_mining.csv"
}