{ "bcoid": "GLY_000245", "title": "Rat UniProtKB Xref PDB", "description": "The Rat UniProtKB Xref PDB contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Pdb cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P01946-1...", "protein_xref..." ], [ "P01946-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_label" } ], [ "P01946-1", "protein_xref_pdb", "3DHT", "" ], [ "P01946-1", "protein_xref_pdb", "3HF4", "" ], [ "P02761-1", "protein_xref_pdb", "2A2G", "" ], [ "P02761-1", "protein_xref_pdb", "2A2U", "" ], [ "P02767-1", "protein_xref_pdb", "1GKE", "" ], [ "P02767-1", "protein_xref_pdb", "1IE4", "" ], [ "P02767-1", "protein_xref_pdb", "1KGI", "" ], [ "P02767-1", "protein_xref_pdb", "1KGJ", "" ], [ "P02767-1", "protein_xref_pdb", "1RVS", "" ], [ "P02767-1", "protein_xref_pdb", "2M5K", "" ], [ "P02767-1", "protein_xref_pdb", "2M5M", "" ], [ "P02767-1", "protein_xref_pdb", "3ZPK", "" ], [ "Q02874-1", "protein_xref_pdb", "1YD9", "" ], [ "P08011-1", "protein_xref_pdb", "2H8A", "" ], [ "P08011-1", "protein_xref_pdb", "5I9K", "" ], [ "P08011-1", "protein_xref_pdb", "5IA9", "" ], [ "P22002-1", "protein_xref_pdb", "1VYT", "" ], [ "Q02294-1", "protein_xref_pdb", "4DEX", "" ], [ "Q02293-1", "protein_xref_pdb", "1D8D", "" ], [ "Q02293-1", "protein_xref_pdb", "1D8E", "" ], [ "Q02293-1", "protein_xref_pdb", "1KZO", "" ], [ "Q02293-1", "protein_xref_pdb", "1KZP", "" ], [ "Q02293-1", "protein_xref_pdb", "1FPP", "" ], [ "Q02293-1", "protein_xref_pdb", "1FT1", "" ], [ "Q02293-1", "protein_xref_pdb", "1FT2", "" ], [ "Q02293-1", "protein_xref_pdb", "1FTI", "" ], [ "Q02293-1", "protein_xref_pdb", "1HZ7", "" ], [ "Q02293-1", "protein_xref_pdb", "1JCR", "" ], [ "Q02293-1", "protein_xref_pdb", "1JCS", "" ], [ "Q02293-1", "protein_xref_pdb", "1KZR", "" ], [ "Q02293-1", "protein_xref_pdb", "1N94", "" ], [ "Q02293-1", "protein_xref_pdb", "1N95", "" ], [ "Q02293-1", "protein_xref_pdb", "1N9A", "" ], [ "Q02293-1", "protein_xref_pdb", "1NI1", "" ], [ "Q02293-1", "protein_xref_pdb", "1NL4", "" ], [ "Q02293-1", "protein_xref_pdb", "1O1R", "" ], [ "Q02293-1", "protein_xref_pdb", "1O1S", "" ], [ "Q02293-1", "protein_xref_pdb", "1O1T", "" ], [ "Q02293-1", "protein_xref_pdb", "1O5M", "" ], [ "Q02293-1", "protein_xref_pdb", "1QBQ", "" ], [ "Q02293-1", "protein_xref_pdb", "1QE2", "" ], [ "Q02293-1", "protein_xref_pdb", "1SA5", "" ], [ "Q02293-1", "protein_xref_pdb", "1TN7", "" ], [ "Q02293-1", "protein_xref_pdb", "1TN8", "" ], [ "Q02293-1", "protein_xref_pdb", "1X81", "" ], [ "Q02293-1", "protein_xref_pdb", "2BED", "" ], [ "Q02293-1", "protein_xref_pdb", "2FTI", "" ], [ "Q02293-1", "protein_xref_pdb", "2R2L", "" ], [ "Q02293-1", "protein_xref_pdb", "2ZIR", "" ], [ "Q02293-1", "protein_xref_pdb", "2ZIS", "" ], [ "Q02293-1", "protein_xref_pdb", "3DPY", "" ], [ "Q02293-1", "protein_xref_pdb", "3E30", "" ], [ "Q02293-1", "protein_xref_pdb", "3E32", "" ], [ "Q02293-1", "protein_xref_pdb", "3E33", "" ], [ "Q02293-1", "protein_xref_pdb", "3E34", "" ], [ "Q02293-1", "protein_xref_pdb", "3EU5", "" ], [ "Q02293-1", "protein_xref_pdb", "3EUV", "" ], [ "Q02293-1", "protein_xref_pdb", "3FTI", "" ], [ "Q02293-1", "protein_xref_pdb", "3KSL", "" ], [ "Q02293-1", "protein_xref_pdb", "3KSQ", "" ], [ "Q02293-1", "protein_xref_pdb", "4GTM", "" ], [ "Q02293-1", "protein_xref_pdb", "4GTO", "" ], [ "Q02293-1", "protein_xref_pdb", "4GTP", "" ], [ "Q02293-1", "protein_xref_pdb", "4GTQ", "" ], [ "Q02293-1", "protein_xref_pdb", "4GTR", "" ], [ "D4A133-1", "protein_xref_pdb", "6VQ6", "" ], [ "D4A133-1", "protein_xref_pdb", "6VQ7", "" ], [ "D4A133-1", "protein_xref_pdb", "6VQ8", "" ], [ "D4A133-1", "protein_xref_pdb", "6VQ9", "" ], [ "D4A133-1", "protein_xref_pdb", "6VQA", "" ], [ "D4A133-1", "protein_xref_pdb", "6VQB", "" ], [ "Q9Z270-1", "protein_xref_pdb", "1Z9L", "" ], [ "Q9Z270-1", "protein_xref_pdb", "1Z9O", "" ], [ "Q9Z272-1", "protein_xref_pdb", "6IUH", "" ], [ "Q9Z272-1", "protein_xref_pdb", "2JX0", "" ], [ "Q9Z272-1", "protein_xref_pdb", "2W6A", "" ], [ "Q9Z272-1", "protein_xref_pdb", "6IUI", "" ], [ "Q00972-1", "protein_xref_pdb", "1GJV", "" ], [ "Q00972-1", "protein_xref_pdb", "1GKX", "" ], [ "Q00972-1", "protein_xref_pdb", "1GKZ", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ0", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ2", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ4", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ5", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref PDB\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.971888\n\nModified on\n - 2022-01-19T13:01:25.317411\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.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 Rat UniProtKB Xref PDB contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to PDB database accessions/identifiers. The dataset is derived from 2019-09 UniProtKB release. 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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: rat_protein_uniprot-proteome-rattus-norvegicus.ntcsv\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/rat_protein_ntdata.nt\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org//ln2downloads/ebi/2021_03/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_pdb.csv\n Name: rat_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_pdb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_pdb.csv" }