{
    "bcoid": "GLY_000331",
    "title": "Rat Glycosylation Sites (GlyConnect) ",
    "description": "The Rat Glycosylation Sites (GlyConnect) dataset contains rat [taxid:10116] UniProtKB canonical accessions ...",
    "filename": "rat_proteoform_glycosylation_sites_glyconnect.csv",
    "filetype": "csv",
    "categories": {
        "species": "Rattus norvegicus",
        "molecule": "Proteoform",
        "tags": "Glycosylation Sites",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "P48199-1...",
                "N-Linked..."
            ],
            [
                "P48199-1...",
                "N-Linked..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "glycosylatio..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "glycosylation_type"
                },
                {
                    "type": "string",
                    "label": "saccharide"
                },
                {
                    "type": "string",
                    "label": "amino_acid"
                },
                {
                    "type": "string",
                    "label": "glycosylation_site_uniprotkb"
                },
                {
                    "type": "string",
                    "label": "evidence"
                },
                {
                    "type": "string",
                    "label": "composition"
                },
                {
                    "type": "string",
                    "label": "glyconnect_id"
                },
                {
                    "type": "string",
                    "label": "is_composition_only"
                },
                {
                    "type": "string",
                    "label": "glycan_core"
                },
                {
                    "type": "string",
                    "label": "glyconnect_protein_id"
                },
                {
                    "type": "string",
                    "label": "glytoucan_ac_composition"
                }
            ],
            [
                "P48199-1",
                "N-Linked",
                "G76675AB",
                "Asn",
                "147",
                "8486673",
                "Hex:5 HexNAc:4 NeuAc:1",
                "1080",
                "",
                "Complex",
                "114",
                "G06356OH"
            ],
            [
                "P48199-1",
                "N-Linked",
                "G84467IZ",
                "Asn",
                "147",
                "8486673",
                "Hex:5 HexNAc:4 NeuAc:2",
                "1378",
                "",
                "Complex",
                "114",
                "G48414YA"
            ]
        ]
    },
    "readme": "Name\n   - Rat Glycosylation Sites (GlyConnect) \n\nVersion\n   - 1.5.18\n\nCreated on\n  - 2020-02-10T12:21:08.095461\n\nModified on\n   - 2020-02-10T12:45:27.721901\n\nCreated by\n   - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n   - Frederique Lisacek [frederique.lisacek@sib.swiss], Julien Mariethoz [julien.mariethoz@sib.swiss]\n\nChecksum\n   - \n\nUsability Domain\n   - The Rat Glycosylation Sites (GlyConnect) dataset contains rat [taxid:10116] UniProtKB canonical accessions with information on reported glycosylation sites in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived directly from authors ( Frederique Lisacek; Julien Mariethoz) on 10/09/2019. If you use this dataset please provide proper attribution to GlyConnect and GlyGen.\n\nDescription Domain\n   Keywords\n   - glycosylation\n   - reported glycosylation\n\n   Pipeline Steps\n   - Step-1: The script loads the glycosylation information from the input JSON file and extracts the data associated with Rat [TaxID:10116] UniProtKB accessions. The QC checks filter out any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000244) and/or if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence provided in the 2019-09 UniProtKB release for that protein.\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: glygen_2019_10_09_56_06.json\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/source/glygen_2019_10_09_56_06.json\n      Name: rat_protein_masterlist.csv\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/rat_protein_masterlist.csv\n      Name: rat_protein_canonicalsequences.fasta\n      URI: https://data.glygen.org/reviewed/rat_protein_canonicalsequences.fasta\n   Output Subdomain\n      Name: rat_proteoform_glycosylation_sites_glyconnect.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv\n      Name: rat_proteoform_glycosylation_sites_glyconnect.stat.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.5.18/reviewed/rat_proteoform_glycosylation_sites_glyconnect.stat.csv\n\nFields\n      Name: \"glyconnect_id\"\n     Description: \"entity Id from GlyConnect database\"\n      Unique Values: \"2\"\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: \"1\"\n      Name: \"glycosylation_site_uniprotkb\"\n     Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n      Unique Values: \"1\"\n      Name: \"glycosylation_type\"\n     Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n      Unique Values: \"1\"\n      Name: \"amino_acid\"\n     Description: \"Three letter abbreviation code of the amino acid\"\n      Unique Values: \"1\"\n      Name: \"glycan_core\"\n     Description: \"Core of the associated glycan\"\n      Unique Values: \"1\"\n      Name: \"evidence\"\n     Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n      Unique Values: \"1\"\n      Name: \"saccharide\"\n     Description: \"Sugar\"\n      Unique Values: \"2\"\n      Name: \"glyconnect_protein_id\"\n     Description: \"Protein  id from GlyConnect database\"\n      Unique Values: \"1\"\n      Name: \"is_composition_only\"\n     Description: \"Yes when the associated GlytouCan accession is a composition accession only.\"\n      Unique Values: \"1\"\n      Name: \"glytoucan_ac_composition\"\n     Description: \"Composition of the associated glycan from GlyConnect database\"\n      Unique Values: \"2\"\n      Name: \"composition\"\n     Description: \"Composition of glycan\"\n      Unique Values: \"2\"",
    "downloadurl": "/ln2data/releases/data/v-1.5.18/reviewed/rat_proteoform_glycosylation_sites_glyconnect.csv"
}