{
    "bcoid": "GLY_000143",
    "title": "Human Protein Glycosylation (Literature)",
    "description": "The dataset provides information on N-glycosylation sites on Human proteins. The data has been processed ...",
    "filename": "human_proteoform_glycosylation_sites_literature.csv",
    "filetype": "csv",
    "categories": {
        "species": "Homo sapiens",
        "molecule": "Proteoform",
        "tags": "UniCarbKB publications",
        "status": "Reviewed",
        "file_type": "csv",
        "scope": "external"
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                "Q13443-1...",
                "144..."
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        "headers": [
            "uniprotkb_ca...",
            "glycosylatio..."
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        "colwidth": [
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            "20%"
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                "GLYDS000143",
                "A8MVE2",
                "24190977",
                "NLS",
                "NXS"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q8NHL6-3",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q8NHL6-3",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q8NHL6-2",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q8NHL6-2",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q8NHL6",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q8NHL6",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A8MVE2",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "Q8NHL6-1",
                "281",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A8MVE2",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "O76082-1",
                "91",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "O76082",
                "24190977",
                "NFS",
                "NXS"
            ],
            [
                "O76082-1",
                "91",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "O76082",
                "24190977",
                "NFS",
                "NXS"
            ],
            [
                "Q9H015-1",
                "91",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q9H015",
                "24190977",
                "NFS",
                "NXS"
            ],
            [
                "Q9H015-1",
                "91",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q9H015",
                "24190977",
                "NFS",
                "NXS"
            ],
            [
                "O76082-1",
                "91",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "F8WCC9",
                "24190977",
                "NFS",
                "NXS"
            ],
            [
                "O76082-1",
                "91",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "F8WCC9",
                "24190977",
                "NFS",
                "NXS"
            ],
            [
                "A2RU67-1",
                "396",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2RU67",
                "24190977",
                "NCS",
                "NXS"
            ],
            [
                "A2RU67-1",
                "396",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2RU67",
                "24190977",
                "NCS",
                "NXS"
            ],
            [
                "A2RU67-1",
                "399",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2RU67",
                "24190977",
                "NLL",
                "other"
            ],
            [
                "A2RU67-1",
                "399",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2RU67",
                "24190977",
                "NLL",
                "other"
            ],
            [
                "A2RU67-1",
                "237",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2RU67",
                "24190977",
                "NAT",
                "NXT"
            ],
            [
                "A2RU67-1",
                "237",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2RU67",
                "24190977",
                "NAT",
                "NXT"
            ],
            [
                "Q01973-1",
                "315",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q01973",
                "24190977",
                "NST",
                "NXT"
            ],
            [
                "Q01973-1",
                "315",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "Q01973",
                "24190977",
                "NST",
                "NXT"
            ],
            [
                "A2VDJ0-1",
                "343",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pubmed",
                "24190977",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2VDJ0-5",
                "24190977",
                "NFT",
                "NXT"
            ],
            [
                "A2VDJ0-1",
                "343",
                "Asn",
                "",
                "N-linked",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "protein_xref_glygen_ds",
                "GLYDS000143",
                "A2VDJ0-5",
                "24190977",
                "NFT",
                "NXT"
            ]
        ]
    },
    "readme": "Name\n   - Human Protein Glycosylation (Literature)\n\nVersion\n   - 1.8.25\n\nCreated on\n  - 2019-06-14T14:54:26.195339\n\nModified on\n   - 2019-09-12T16:37:13.572422\n\nCreated by\n   - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n   - \n\nChecksum\n   - \n\nUsability Domain\n   - The dataset provides information on N-glycosylation sites on Human proteins. The data has been processed from the supplementary material from 2 publications (1. \"Deeb, S. J., Cox, J., Schmidt-Supprian, M., & Mann, M. (2013). N-linked Glycosylation Enrichment for In-depth Cell Surface Proteomics of Diffuse Large B-cell Lymphoma Subtypes. Molecular & Cellular Proteomics, 13(1), 240-251. doi:10.1074/mcp.m113.033977\" 2. \"Boersema, P. J., Geiger, T., Wi?niewski, J. R., & Mann, M. (2012). Quantification of theN-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Human Blood Samples. Molecular & Cellular Proteomics, 12(1), 158-171. doi:10.1074/mcp.m112.023614\").  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\n   - literature\n   - publications\n\n   Pipeline Steps\n   - Step-1: The supplementary tables from two publications were downloaded and columns \"protein\" and \"site\" were extracted, and additional column evidence where values=\"the respective PMIDs\" was added to produce the input files. A python script was developed process input files 1. to map the UniProtKB accessions to UniProtKB canonical accessions 2. Check position+amino acid with the canonical fasta sequences (https://data.glygen.org/GLYDS000002)to generate the output files.\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: glycosylation_sites_24190977_s5.csv\n      URI: https://data.glygen.org/ln2wwwdata/source/glycosylation_sites_24190977_s5.csv\n      Name: glycosylation_sites_23090970_s5.csv\n      URI: https://data.glygen.org/ln2wwwdata/source/glycosylation_sites_23090970_s5.csv\n      Name: glycosylation_sites_23090970_s2.csv\n      URI: https://data.glygen.org/ln2wwwdata/source/glycosylation_sites_23090970_s2.csv\n   Output Subdomain\n      Name: human_proteoform_glycosylation_sites_literature.csv\n      URI: http://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_glycosylation_sites_literature.csv\n      Name: human_proteoform_glycosylation_sites_literature.stat.csv\n      URI: http://data.glygen.org/ln2wwwdata/reviewed/human_proteoform_glycosylation_sites_literature.stat.csv\n\nFields\n      Name: \"src_xref_key\"\n     Description: \"Source Xref  key\"\n      Unique Values: \"1\"\n      Name: \"xref_id\"\n     Description: \"ID of the X-ref\"\n      Unique Values: \"119\"\n      Name: \"title\"\n     Description: \"Title of the published article in the journal\"\n      Unique Values: \"119\"\n      Name: \"src_xref_id\"\n     Description: \"Source X-ref ID\"\n      Unique Values: \"120\"\n      Name: \"journal_name\"\n     Description: \"The name of the journal in which the article is published\"\n      Unique Values: \"49\"\n      Name: \"authors\"\n     Description: \"NA\"\n      Unique Values: \"118\"\n      Name: \"publication_date\"\n     Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n      Unique Values: \"117\"\n      Name: \"glytoucan_ac\"\n     Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n      Unique Values: \"115\"\n      Name: \"xref_key\"\n     Description: \"Source key associated to the  xref_id\"\n      Unique Values: \"1\"",
    "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/human_proteoform_glycosylation_sites_literature.csv"
}
