{
    "bcoid": "GLY_001152",
    "title": "Pig Predicted O-Glycosylation Sites (IsoGlyP)",
    "description": "The Pig Predicted O-Glycosylation Sites dataset contains predicted Sus scrofa (TaxID: 9823) O-linked ...",
    "filename_list": "pig_proteoform_glycosylation_sites_predicted_isoglyp.csv",
    "filename": "pig_proteoform_glycosylation_sites_predicted_isoglyp.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Sus scrofa"
        ],
        "molecule": [
            "Proteoform"
        ],
        "tag": [
            "O-Glycosylation Sites"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "glycosylation_sites_"
        ]
    },
    "minitable": {
        "content": [
            [
                "A0A5G2RA74-1...",
                "581..."
            ],
            [
                "A0A5G2RA74-1...",
                "583..."
            ]
        ],
        "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_key"
                },
                {
                    "type": "string",
                    "label": "xref_id"
                },
                {
                    "type": "string",
                    "label": "src_xref_key"
                },
                {
                    "type": "string",
                    "label": "src_xref_id"
                },
                {
                    "type": "string",
                    "label": "start_pos"
                },
                {
                    "type": "string",
                    "label": "end_pos"
                },
                {
                    "type": "string",
                    "label": "start_aa"
                },
                {
                    "type": "string",
                    "label": "end_aa"
                },
                {
                    "type": "string",
                    "label": "isoform_mapping_notes"
                }
            ],
            [
                "A0A5G2RA74-1",
                "581",
                "Thr",
                "",
                "O-linked",
                "protein_xref_glygen_ds",
                "GLY_001152",
                "protein_xref_glygen_ds",
                "GLY_001152",
                "581",
                "581",
                "Thr",
                "Thr",
                ""
            ],
            [
                "A0A5G2RA74-1",
                "583",
                "Thr",
                "",
                "O-linked",
                "protein_xref_glygen_ds",
                "GLY_001152",
                "protein_xref_glygen_ds",
                "GLY_001152",
                "583",
                "583",
                "Thr",
                "Thr",
                ""
            ]
        ]
    },
    "readme": "Name\n   - Pig Predicted O-Glycosylation Sites (IsoGlyP)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2024-08-01T15:51:45\n\nModified on\n   - 2024-12-05T16:18:55.533Z\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 Pig Predicted O-Glycosylation Sites dataset contains predicted Sus scrofa (TaxID: 9823) O-linked Glycosylation sites derived from the IsoGlyP tool and mapped to UniProtKB canonical accessions . This tool was developed by Jonathon E Mohl and colleagues and aims to identify position-specific enhancement values that are derived from GalNAc-T isoform-specific amino acid preferences in order to estimate the likelihood of a site being glycosylated by a specific transferase. Predicted sites included in the dataset were selected based on meeting a stringent EVP threshold score of 10 or higher (https://isoglyp.utep.edu/).\n\nDescription Domain\n   Keywords\n   - O-Glycosylation\n   - Predicted\n\n   Pipeline Steps\n   - Step-1: The script takes a path twords a canonical sequences fasta and runs it through the IsoGlyP O-Glycosylation prediction software. This process is slow so it is broken into 10 seperate processes.\n   - Step-2: The script takes the output of the previous step and combines them into one final dataset.\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/\n   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/\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: output.pig.csv\n      URI: https:/data.glygen.org/ln2downloads/isoglyp/outputdb/output.pig.csv\n      Name: output.pig_legacy.csv\n      URI: https:/data.glygen.org/ln2downloads/isoglyp/outputdb/output.pig_legacy.csv\n   Output Subdomain\n      Name: pig_proteoform_glycosylation_sites_predicted_isoglyp.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/pig_proteoform_glycosylation_sites_predicted_isoglyp.csv\n      Name: pig_proteoform_glycosylation_sites_predicted_isoglyp.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/pig_proteoform_glycosylation_sites_predicted_isoglyp.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"4283\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/pig_proteoform_glycosylation_sites_predicted_isoglyp.csv"
}