{
    "bcoid": "GLY_000403",
    "title": "HCV1b N-Glycosylation Sequon",
    "description": "The Hepatitis C virus (genotype 1b, isolate Japanese) N-Glycosylation Sequon dataset contains N-glycosylation ...",
    "filename": "hcv1b_protein_glycosylation_motifs.csv",
    "filetype": "csv",
    "categories": {
        "species": "Hepatitis C virus (genotype 1b, isolate Japanese)",
        "molecule": "Protein",
        "tags": "N-Glycosylation Sequon",
        "file_type": "csv",
        "status": "Reviewed",
        "scope": "internal"
    },
    "minitable": {
        "content": [
            [
                "P26662-1...",
                "196..."
            ],
            [
                "P26662-1...",
                "209..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "start_pos..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "start_pos"
                },
                {
                    "type": "string",
                    "label": "end_pos"
                },
                {
                    "type": "string",
                    "label": "motif"
                }
            ],
            [
                "P26662-1",
                "196",
                "198",
                "NVS"
            ],
            [
                "P26662-1",
                "209",
                "211",
                "NSS"
            ],
            [
                "P26662-1",
                "234",
                "236",
                "NFS"
            ],
            [
                "P26662-1",
                "250",
                "252",
                "NSS"
            ],
            [
                "P26662-1",
                "305",
                "307",
                "NCS"
            ],
            [
                "P26662-1",
                "325",
                "327",
                "NWS"
            ],
            [
                "P26662-1",
                "417",
                "419",
                "NGS"
            ],
            [
                "P26662-1",
                "423",
                "425",
                "NRT"
            ],
            [
                "P26662-1",
                "430",
                "432",
                "NDS"
            ],
            [
                "P26662-1",
                "448",
                "450",
                "NAS"
            ],
            [
                "P26662-1",
                "532",
                "534",
                "NET"
            ],
            [
                "P26662-1",
                "556",
                "558",
                "NST"
            ],
            [
                "P26662-1",
                "576",
                "578",
                "NNT"
            ],
            [
                "P26662-1",
                "623",
                "625",
                "NFT"
            ],
            [
                "P26662-1",
                "645",
                "647",
                "NWT"
            ],
            [
                "P26662-1",
                "1213",
                "1215",
                "NSS"
            ],
            [
                "P26662-1",
                "2041",
                "2043",
                "NGS"
            ],
            [
                "P26662-1",
                "2077",
                "2079",
                "NYS"
            ],
            [
                "P26662-1",
                "2240",
                "2242",
                "NIT"
            ],
            [
                "P26662-1",
                "2788",
                "2790",
                "NVS"
            ]
        ]
    },
    "readme": "Name\n   - HCV1b N-Glycosylation Sequon\n\nVersion\n   - 1.5.30\n\nCreated on\n  - 2020-03-20T12:45:33.474142\n\nModified on\n   - 2020-04-09T18:15:36.917227\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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 Hepatitis C virus (genotype 1b, isolate Japanese) N-Glycosylation Sequon dataset contains N-glycosylation sequon or motif or consensus sequence for hcv1b [taxid:11116] UniProtKB canonical sequences identified by the script. The script identifies the N-glycosylation sequon pattern - Asn-X-Ser/Thr , where X is any amino acid except proline (Pro) for UniProtKB accessions. The dataset is derived form 2019-09 UniprotKB release.\n\nDescription Domain\n   Keywords\n   - n-glycosylation sequon\n   - NXS/T\n   - n-glycosylation motif\n   - n-glycosylation consensus sequence\n\n   Pipeline Steps\n   - Step-1: The script uses the PS Scan tool (accession- PS00001) from ProSite to extracts the N-glycosylation pattern/sequon/motif N-{P}-[ST]-{P} where P is not a proline from the UniProtKB canonical sequences. More info -  https://prosite.expasy.org/PDOC00001, https://prosite.expasy.org/PS00001 and extracts as a csv.\n\nExecution Domain\n   Scripts   - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: hcv1b_protein_canonicalsequences.fasta\n      URI: https://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/hcv1b_protein_canonicalsequences.fasta\n   Output Subdomain\n      Name: hcv1b_protein_glycosylation_motifs.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/hcv1b_protein_glycosylation_motifs.csv\n      Name: hcv1b_protein_glycosylation_motifs.stat.csv\n      URI: http://data.glygen.org/ln2data/releases/data/v-1.5.30/reviewed/hcv1b_protein_glycosylation_motifs.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: \"1\"\n      Name: \"end_pos\"\n     Description: \"End position of the gene on the chromosome\"\n      Unique Values: \"20\"\n      Name: \"motif\"\n     Description: \"Glycan motif\"\n      Unique Values: \"16\"\n      Name: \"start_pos\"\n     Description: \"Start position of the gene on the chromosome\"\n      Unique Values: \"20\"",
    "downloadurl": "/ln2data/releases/data/v-1.5.30/reviewed/hcv1b_protein_glycosylation_motifs.csv"
}