{ "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": [ [ "Q9WUD2-1...", "2ETA..." ], [ "Q9WUD2-1...", "2ETB..." ] ], "headers": [ "uniprotkb_ca...", "database_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "database_label" } ], [ "Q9WUD2-1", "2ETA", "" ], [ "Q9WUD2-1", "2ETB", "" ], [ "Q9WUD2-1", "2ETC", "" ], [ "Q9WUD2-1", "5HI9", "" ], [ "Q9WUD2-1", "6BO4", "" ], [ "Q9WUD2-1", "6BO5", "" ], [ "O55043-1", "2AK5", "" ], [ "O55043-1", "2P4R", "" ], [ "O55043-1", "2DF6", "" ], [ "O55043-1", "2G6F", "" ], [ "O55043-1", "2W6B", "" ], [ "O55043-1", "3L4F", "" ], [ "O55043-1", "3QJN", "" ], [ "P01946-1", "3DHT", "" ], [ "P01946-1", "3HF4", "" ], [ "P20646-1", "1RPA", "" ], [ "P20646-1", "1RPT", "" ], [ "P02767-1", "1GKE", "" ], [ "P02767-1", "1IE4", "" ], [ "P02767-1", "1KGI", "" ], [ "P02767-1", "1KGJ", "" ], [ "P02767-1", "1RVS", "" ], [ "P02767-1", "2M5K", "" ], [ "P02767-1", "2M5M", "" ], [ "P02767-1", "3ZPK", "" ], [ "P24135-1", "2EOB", "" ], [ "Q63009-1", "1OR8", "" ], [ "Q63009-1", "1ORH", "" ], [ "Q63009-1", "1ORI", "" ], [ "Q63009-1", "3Q7E", "" ], [ "Q8VHW5-1", "6QKC", "" ], [ "Q8VHW5-1", "6QKZ", "" ], [ "Q62717-1", "6A68", "" ], [ "P40307-1", "6EPC", "" ], [ "P40307-1", "6EPD", "" ], [ "P40307-1", "6EPE", "" ], [ "P40307-1", "6EPF", "" ], [ "Q9R064-1", "4KFW", "" ], [ "P24473-1", "1R4W", "" ], [ "P49791-1", "3CH5", "" ], [ "P49791-1", "3GJ3", "" ], [ "P49791-1", "3GJ4", "" ], [ "P49791-1", "3GJ5", "" ], [ "P49791-1", "3GJ6", "" ], [ "P49791-1", "3GJ7", "" ], [ "P49791-1", "3GJ8", "" ], [ "P49791-1", "2K0C", "" ], [ "P00173-1", "1AQA", "" ], [ "P00173-1", "1AW3", "" ], [ "P00173-1", "1AXX", "" ], [ "P00173-1", "1B5A", "" ], [ "P00173-1", "1B5B", "" ], [ "P00173-1", "1BFX", "" ], [ "P00173-1", "1BLV", "" ], [ "P00173-1", "1I87", "" ], [ "P00173-1", "1I8C", "" ], [ "P00173-1", "1IB7", "" ], [ "P00173-1", "1IET", "" ], [ "P00173-1", "1IEU", "" ], [ "P00173-1", "1JEX", "" ], [ "P00173-1", "1MNY", "" ], [ "P00173-1", "2AXX", "" ], [ "P00173-1", "5XE4", "" ], [ "P00173-1", "5XEE", "" ], [ "P49799-1", "1AGR", "" ], [ "P49799-1", "1EZT", "" ], [ "P49799-1", "1EZY", "" ], [ "Q71RJ2-1", "5KK2", "" ], [ "Q71RJ2-1", "5VOT", "" ], [ "Q71RJ2-1", "5VOU", "" ], [ "Q71RJ2-1", "5VOV", "" ], [ "Q71RJ2-1", "6NJL", "" ], [ "Q71RJ2-1", "6NJM", "" ], [ "Q71RJ2-1", "6NJN", "" ], [ "P02761-1", "2A2G", "" ], [ "P02761-1", "2A2U", "" ], [ "P53563-1", "1AF3", "" ], [ "P53563-1", "4QNQ", "" ], [ "P08523-1", "1JYT", "" ], [ "P08523-1", "1ZRI", "" ], [ "P15431-1", "6DW0", "" ], [ "P15431-1", "6DW1", "" ], [ "P18113-1", "3M9E", "" ], [ "P07872-1", "1IS2", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref PDB\n\nVersion\n - 1.5.23\n\nCreated on\n - 2019-09-06T14:06:38.971888\n\nModified on\n - 2020-04-10T11:58:31.122542\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]\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: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/source/uniprot-proteome-rattus-norvegicus.nt\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_uniprot-proteome-rattus-norvegicus.ntcsv\n Output Subdomain\n Name: rat_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_xref_pdb.csv\n Name: rat_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"642\"\n Name: \"database_label\"\n Description: \"Label or name assigned to the corresponding identifier in the source database\"\n Unique Values: \"1\"\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"3157\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/rat_protein_xref_pdb.csv" }