{
    "bcoid": "GLY_001390",
    "title": "Zebrafish GlyGen-PDB Cross References Mapping",
    "description": "The Zebrafish UniProtKB Xref PDB contains Danio rerio [taxid:7955] UniProtKB canonical accessions cross-referenced ...",
    "filename_list": "zebrafish_protein_pdb_map.csv",
    "filename": "zebrafish_protein_pdb_map.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Danio rerio"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Pdb cross-references"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q6PBK3-1...",
                "region_1..."
            ],
            [
                "Q6PBK3-1...",
                "region_1..."
            ]
        ],
        "headers": [
            "uniprotkb_ca...",
            "sequence_reg..."
        ],
        "colwidth": [
            "40%",
            "20%"
        ]
    },
    "sampledata": {
        "type": "table",
        "data": [
            [
                {
                    "type": "string",
                    "label": "uniprotkb_canonical_ac"
                },
                {
                    "type": "string",
                    "label": "sequence_region"
                },
                {
                    "type": "string",
                    "label": "pdb_id"
                },
                {
                    "type": "string",
                    "label": "pdb_chain"
                },
                {
                    "type": "string",
                    "label": "start_pos"
                },
                {
                    "type": "string",
                    "label": "end_pos"
                },
                {
                    "type": "string",
                    "label": "overlap_ratio"
                },
                {
                    "type": "string",
                    "label": "overlap_category"
                },
                {
                    "type": "string",
                    "label": "experimental_method"
                },
                {
                    "type": "string",
                    "label": "resolution"
                },
                {
                    "type": "string",
                    "label": "selection_flag"
                }
            ],
            [
                "Q6PBK3-1",
                "region_1",
                "7oyb",
                "c2",
                "1",
                "69",
                "1.0",
                "0.75",
                "Electron_Microscopy",
                "2.4",
                "True"
            ],
            [
                "Q6PBK3-1",
                "region_1",
                "7oya",
                "c2",
                "1",
                "69",
                "1.0",
                "0.75",
                "Electron_Microscopy",
                "3.2",
                "False"
            ]
        ]
    },
    "readme": "Name\n   - Zebrafish GlyGen-PDB Cross References Mapping\n\nVersion\n   - v-2.9.1\n\nCreated on\n  - 2025-03-21T10:43:09\n\nModified on\n   - 2025-03-21T10:44:04.705Z\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 Zebrafish UniProtKB Xref PDB contains Danio rerio [taxid:7955] UniProtKB canonical accessions cross-referenced to PDB database accessions/identifiers. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen.\n   - The Protein Data Bank is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. \n\nDescription Domain\n   Keywords\n   - protein 3D structure\n   - RCSB PDB\n   - cross-reference\n\n   Pipeline Steps\n   - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to RCSB PDB database accessions/identifiers from the triplestore containing triples from nt file and extracts the data as a csv dataset. \n\nExecution Domain\n   Scripts   - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/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: zebrafish_protein_xref_alphafolddb.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/zebrafish_protein_xref_alphafolddb.csv\n   Output Subdomain\n      Name: zebrafish_protein_pdb_map.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/zebrafish_protein_pdb_map.csv\n      Name: zebrafish_protein_pdb_map.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/zebrafish_protein_pdb_map.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\n     Description: \"\"\n      Unique Values: \"198\"\n      Name: \"sequence_region\"\n     Description: \"\"\n      Unique Values: \"2\"\n      Name: \"pdb_id\"\n     Description: \"PDB ID associated with the UniProtKB accession.\"\n      Unique Values: \"535\"\n      Name: \"pdb_chain\"\n     Description: \"\"\n      Unique Values: \"78\"\n      Name: \"start_pos\"\n     Description: \"Start position of the gene on the chromosome\"\n      Unique Values: \"101\"\n      Name: \"end_pos\"\n     Description: \"End position of the gene on the chromosome\"\n      Unique Values: \"190\"\n      Name: \"overlap_ratio\"\n     Description: \"\"\n      Unique Values: \"33\"\n      Name: \"overlap_category\"\n     Description: \"\"\n      Unique Values: \"4\"\n      Name: \"experimental_method\"\n     Description: \"\"\n      Unique Values: \"3\"\n      Name: \"resolution\"\n     Description: \"\"\n      Unique Values: \"172\"\n      Name: \"selection_flag\"\n     Description: \"\"\n      Unique Values: \"2\"",
    "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/zebrafish_protein_pdb_map.csv"
}