{
    "bcoid": "GLY_001304",
    "title": "Zebrafish Glycosylation Sites (RCSB PDB)",
    "description": "The Zebrafish Glycosylation Sites (RCSB PDB) dataset contains Danio rerio [taxid:7955] proteins glycosites ...",
    "filename_list": "zebrafish_proteoform_glycosylation_sites_pdb.csv",
    "filename": "zebrafish_proteoform_glycosylation_sites_pdb.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Danio rerio"
        ],
        "molecule": [
            "Proteoform"
        ],
        "tag": [
            "Glycosylation Sites"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [],
        "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": "glycosylation_site_pdb"
                },
                {
                    "type": "string",
                    "label": "carb_name"
                },
                {
                    "type": "string",
                    "label": "n_sequon"
                },
                {
                    "type": "string",
                    "label": "n_sequon_type"
                },
                {
                    "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"
                }
            ]
        ]
    },
    "readme": "Name\n   - Zebrafish Glycosylation Sites (RCSB PDB)\n\nVersion\n   - v-2.8.1\n\nCreated on\n  - 2019-01-23T17:21:05.909814\n\nModified on\n   - 2024-12-10T16:57:20.331Z\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   - Jasmine Young [jasmine@rcsb.rutgers.edu], Chenghua Shao [chenghua@rcsb.rutgers.edu]\n\nChecksum\n   - \n\nUsability Domain\n   - The Zebrafish Glycosylation Sites (RCSB PDB) dataset contains Danio rerio [taxid:7955] proteins glycosites mapped from the associated RCSB PDB Id's using SIFTS database (https://www.ebi.ac.uk/pdbe/docs/sifts/). The glycosylation data (PDB ID, GlycoSite, Chain ID, Sugar (first link)) was retrieved from RCSB group. [www.rcsb.org, Nucleic Acids Research, 28: 235-242.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472/)].\n\nDescription Domain\n   Keywords\n   - PDB\n   - glycosylation sites\n   - amino acid\n   - amino acid chain\n\n   Pipeline Steps\n   - Step-1: The script extracts the PDB IDs and PDB glycosite from the input .tsv files and maps it to the corresponding UniProtKB accessions and position using the coordinate file downloaded from the SIFTS database using the formula:(SP_BEG-RES_BEG)+ PDB-Position)]. The script also validates the UniProtKB glycosite (amino acid + position) with the corresponding fasta sequences downloaded from UniProtKB.\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-2.8.1/misc/n_sequon_info.csv\n      Name: sample_mapping.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/sample_mapping.csv\n      Name: cellosaurus.txt\n      URI: https:/data.glygen.org/ln2downloads/cellosaurus/2025_01_13/cellosaurus.txt\n      Name: N-linked-ARG-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/N-linked-ARG-details\n      Name: N-linked-ASN-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/N-linked-ASN-details\n      Name: O-linked-ASP-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-ASP-details\n      Name: O-linked-GLU-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-GLU-details\n      Name: O-linked-SER-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-SER-details\n      Name: O-linked-THR-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-THR-details\n      Name: O-linked-TYR-details\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-TYR-details\n      Name: pdb_chain_uniprot.csv\n      URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/pdb_chain_uniprot.csv\n   Output Subdomain\n      Name: zebrafish_proteoform_glycosylation_sites_pdb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/zebrafish_proteoform_glycosylation_sites_pdb.csv\n      Name: zebrafish_proteoform_glycosylation_sites_pdb.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/zebrafish_proteoform_glycosylation_sites_pdb.stat.csv\n\nFields",
    "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/zebrafish_proteoform_glycosylation_sites_pdb.csv"
}