{
    "bcoid": "GLY_001505",
    "title": "Bovine Glycosylation Sites and Glycans (RCSB PDB)",
    "description": "The Bovine Glycosylation Sites and Glycans (RCSB PDB) dataset contains Bos taurus [taxid:9913] glycosylation ...",
    "filename_list": "bovine_proteoform_glycosylation_sites_rcsb_pdb.csv",
    "filename": "bovine_proteoform_glycosylation_sites_rcsb_pdb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Bos taurus"
        ],
        "molecule": [
            "Proteoform"
        ],
        "tag": [
            "Glycosylation Sites"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "glycosylation_sites_"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q28146-1...",
                "726..."
            ],
            [
                "Q5NDF2-1...",
                "99..."
            ]
        ],
        "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": "pdb_id"
                },
                {
                    "type": "string",
                    "label": "pdb_extended_id"
                },
                {
                    "type": "string",
                    "label": "amino_acid_chain"
                },
                {
                    "type": "string",
                    "label": "glycosylation_site_pdb"
                },
                {
                    "type": "string",
                    "label": "pdb_glycan_entity_id"
                },
                {
                    "type": "string",
                    "label": "start_pos"
                },
                {
                    "type": "string",
                    "label": "end_pos"
                },
                {
                    "type": "string",
                    "label": "start_aa"
                },
                {
                    "type": "string",
                    "label": "end_aa"
                },
                {
                    "type": "string",
                    "label": "site_seq"
                },
                {
                    "type": "string",
                    "label": "n_sequon"
                },
                {
                    "type": "string",
                    "label": "n_sequon_type"
                },
                {
                    "type": "string",
                    "label": "isoform_mapping_notes"
                }
            ],
            [
                "Q28146-1",
                "726",
                "Ser",
                "",
                "O-linked",
                "protein_xref_pdb",
                "3POY",
                "protein_xref_pdb4glycans",
                "3POY",
                "3POY",
                "pdb_00003poy",
                "A",
                "399",
                "",
                "726",
                "726",
                "Ser",
                "Ser",
                "S",
                "",
                "",
                "reported site S690 is on non-canonical isoform Q28146-7 which maps to canonical isoform site Q28146-1:726"
            ],
            [
                "Q5NDF2-1",
                "99",
                "Asn",
                "",
                "N-linked",
                "protein_xref_pdb",
                "7E9K",
                "protein_xref_pdb4glycans",
                "7E9K",
                "7E9K",
                "pdb_00007e9k",
                "A",
                "58",
                "",
                "99",
                "99",
                "Asn",
                "Asn",
                "N",
                "NAS",
                "NXS",
                ""
            ]
        ]
    },
    "readme": "Name\n   - Bovine Glycosylation Sites and Glycans (RCSB PDB)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2026-01-21T19:42:36\n\nModified on\n   - 2026-08-18T14:36:28.481Z\n\nCreated by\n   - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n   - \n\nChecksum\n   - \n\nUsability Domain\n   - The Bovine Glycosylation Sites and Glycans (RCSB PDB) dataset contains Bos taurus [taxid:9913] glycosylation sites and associated glycans provided by the RCSB PDB database. Data is retrieved using the RCSB PDB Search API (https://search.rcsb.org/#search-api), Data API (https://data.rcsb.org/index.html#data-api) and Sequence Coordinates Server API (https://sequence-coordinates.rcsb.org/#sequence-coordinates-api). If you use this dataset please provide proper attribution to RCSB PDB and GlyGen.\n\nDescription Domain\n   Keywords\n   - glycosylation\n   - reported glycosylation\n   - UniProtKB\n   - PubMed\n   - DOI\n   - GlyTouCan\n   - RCSB PDB\n   - PDB\n\n   Pipeline Steps\n   - Step-1: The script retrieves data from RCSB PDB in three steps: (1) their RCSB PDB Search API (https://search.rcsb.org/#search-api) is used to retrieve any PDB structures with glycosylation data for this species, followed by (2) their RCSB PDB Data API (https://data.rcsb.org/index.html#data-api) to retrieve data on the glycosylated structures identified in step one, including data on the PDB glycosite position, GlyTouCan IDs and publications, and then (3) the RCSB PDB Sequence Coordinates Server API (https://sequence-coordinates.rcsb.org/#sequence-coordinates-api) to map the chain glycosites to the full UniProtKB protein sequence. The script then extracts the data from the API responses to create the dataset.\n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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: n_sequon_info.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/n_sequon_info.csv\n      Name: bovine_glycosites_rcsb_pdb.csv\n      URI: https:/data.glygen.org/ln2downloads/rcsb_pdb/06_11_2026/bovine_glycosites_rcsb_pdb.csv\n   Output Subdomain\n      Name: bovine_proteoform_glycosylation_sites_rcsb_pdb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/bovine_proteoform_glycosylation_sites_rcsb_pdb.csv\n      Name: bovine_proteoform_glycosylation_sites_rcsb_pdb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/bovine_proteoform_glycosylation_sites_rcsb_pdb.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"38\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/bovine_proteoform_glycosylation_sites_rcsb_pdb.csv"
}