{
    "bcoid": "GLY_001610",
    "title": "Arabidopsis Glycosylation Sites and Glycans view (iCn3D)",
    "description": "The Arabidopsis Glycosylation Sites and Glycans view (iCn3D) dataset contains Arabidopsis thaliana [taxid:3702] ...",
    "filename_list": "arabidopsis_proteoform_glycosylation_sites_icn3d.csv",
    "filename": "arabidopsis_proteoform_glycosylation_sites_icn3d.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Arabidopsis thaliana"
        ],
        "molecule": [
            "Proteoform"
        ],
        "tag": [
            "Glycosylation Sites"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "glycosylation_sites_"
        ]
    },
    "minitable": {
        "content": [
            [
                "O22822-1...",
                "177..."
            ],
            [
                "O22822-1...",
                "177..."
            ]
        ],
        "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": "amino_acid_chain"
                },
                {
                    "type": "string",
                    "label": "amino_acid_chain_auth"
                },
                {
                    "type": "string",
                    "label": "glycosylation_site_pdb"
                },
                {
                    "type": "string",
                    "label": "glycosylation_site_auth"
                },
                {
                    "type": "string",
                    "label": "carb_name"
                },
                {
                    "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": "isoform_mapping_notes"
                }
            ],
            [
                "O22822-1",
                "177",
                "Tyr",
                "",
                "O-linked",
                "protein_xref_icn3d4glycosylation",
                "5U6M|B|177",
                "protein_xref_pdb4glycans",
                "5U6M",
                "5U6M",
                "B",
                "B",
                "177",
                "177",
                "BGC",
                "177",
                "177",
                "Y",
                "Y",
                "Y",
                ""
            ],
            [
                "O22822-1",
                "177",
                "Tyr",
                "",
                "O-linked",
                "protein_xref_icn3d4glycosylation",
                "5U6M|A|177",
                "protein_xref_pdb4glycans",
                "5U6M",
                "5U6M",
                "A",
                "A",
                "177",
                "177",
                "BGC",
                "177",
                "177",
                "Y",
                "Y",
                "Y",
                ""
            ]
        ]
    },
    "readme": "Name\n   - Arabidopsis Glycosylation Sites and Glycans view (iCn3D)\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - \n\nModified on\n   - \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 Arabidopsis Glycosylation Sites and Glycans view (iCn3D) dataset contains Arabidopsis thaliana [taxid:3702] proteins glycosites and attached glycans extracted from the RCSB PDB database using their search, data and sequence coordinates API (see GLY_001412). The generated PDB proteoform dataset is used to map the UniProtKB AC and residue position in our proteoform datasets to the PDB ID, author amino acid chain and author glycosylation site residue position, and construct the links to iCn3D (https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=(PDB_ID)&bu=0&command=select .(amino_acid_chain_auth:glycosylation_site_auth);+center+selection;+zoom+selection) where you can view the highlighted glycosylation site within the 3D structure. If you use this dataset please provide proper attribution to PDB, iCn3D and GlyGen.\n   - The I see in 3D (iCn3D) Structure Viewer is an interactive web-based structure analysis tool which synchronizes the display of 3D structures, 2D interactions, and 1D sequences and annotations.\n\nDescription Domain\n   Keywords\n   - glycosylation\n   - reported glycosylation\n   - UniProtKB\n   - PubMed\n   - PDB\n   - 3D Structure\n   - Data view\n   - iCn3D\n\n   Pipeline Steps\n   - Step-1: The script extracts the UniProtKB ACs, UniProtKB residues, PDB IDs, PDB and auth chain IDs, and PDB and auth glycosite information from the input .csv file.\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: arabidopsis_glycosites_rcsb_pdb.csv\n      URI: https:/data.glygen.org/ln2downloads/rcsb_pdb/06_11_2026/arabidopsis_glycosites_rcsb_pdb.csv\n   Output Subdomain\n      Name: arabidopsis_proteoform_glycosylation_sites_icn3d.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/arabidopsis_proteoform_glycosylation_sites_icn3d.csv\n      Name: arabidopsis_proteoform_glycosylation_sites_icn3d.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/arabidopsis_proteoform_glycosylation_sites_icn3d.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"41\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/arabidopsis_proteoform_glycosylation_sites_icn3d.csv"
}