{ "bcoid": "GLY_000792", "title": "Yeast UniProtKB Xref PDB", "description": "The Yeast UniProtKB Xref PDB contains yeast [taxid:559292] UniProtKB canonical accessions cross-referenced ...", "filename": "yeast_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Pdb cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P17122-1...", "protein_xref..." ], [ "P17122-1...", "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" } ], [ "P17122-1", "protein_xref_pdb", "6BZF", "" ], [ "P17122-1", "protein_xref_pdb", "6BZG", "" ], [ "P25373-1", "protein_xref_pdb", "2JAC", "" ], [ "P25373-1", "protein_xref_pdb", "2JAD", "" ], [ "P25373-1", "protein_xref_pdb", "3C1R", "" ], [ "P25373-1", "protein_xref_pdb", "3C1S", "" ], [ "P25373-1", "protein_xref_pdb", "6MWS", "" ], [ "P25372-1", "protein_xref_pdb", "5YKW", "" ], [ "P25372-1", "protein_xref_pdb", "2OE0", "" ], [ "P25372-1", "protein_xref_pdb", "2OE1", "" ], [ "P25372-1", "protein_xref_pdb", "2OE3", "" ], [ "Q00539-1", "protein_xref_pdb", "6N7P", "" ], [ "Q00539-1", "protein_xref_pdb", "7OQE", "" ], [ "Q00539-1", "protein_xref_pdb", "6G90", "" ], [ "Q00539-1", "protein_xref_pdb", "6N7R", "" ], [ "Q00539-1", "protein_xref_pdb", "6N7X", "" ], [ "Q00539-1", "protein_xref_pdb", "7OQC", "" ], [ "Q00539-1", "protein_xref_pdb", "5ZWN", "" ], [ "P40422-1", "protein_xref_pdb", "1I3Q", "" ], [ "P40422-1", "protein_xref_pdb", "1I50", "" ], [ "P40422-1", "protein_xref_pdb", "1I6H", "" ], [ "P40422-1", "protein_xref_pdb", "1K83", "" ], [ "P40422-1", "protein_xref_pdb", "1NIK", "" ], [ "P40422-1", "protein_xref_pdb", "1NT9", "" ], [ "P40422-1", "protein_xref_pdb", "1PQV", "" ], [ "P40422-1", "protein_xref_pdb", "1R5U", "" ], [ "P40422-1", "protein_xref_pdb", "1R9S", "" ], [ "P40422-1", "protein_xref_pdb", "1R9T", "" ], [ "P40422-1", "protein_xref_pdb", "1SFO", "" ], [ "P40422-1", "protein_xref_pdb", "1TWA", "" ], [ "P40422-1", "protein_xref_pdb", "1TWC", "" ], [ "P40422-1", "protein_xref_pdb", "1TWF", "" ], [ "P40422-1", "protein_xref_pdb", "1TWG", "" ], [ "P40422-1", "protein_xref_pdb", "1TWH", "" ], [ "P40422-1", "protein_xref_pdb", "1WCM", "" ], [ "P40422-1", "protein_xref_pdb", "1Y1V", "" ], [ "P40422-1", "protein_xref_pdb", "1Y1W", "" ], [ "P40422-1", "protein_xref_pdb", "1Y1Y", "" ], [ "P40422-1", "protein_xref_pdb", "1Y77", "" ], [ "P40422-1", "protein_xref_pdb", "2B63", "" ], [ "P40422-1", "protein_xref_pdb", "2B8K", "" ], [ "P40422-1", "protein_xref_pdb", "2E2H", "" ], [ "P40422-1", "protein_xref_pdb", "2E2I", "" ], [ "P40422-1", "protein_xref_pdb", "2E2J", "" ], [ "P40422-1", "protein_xref_pdb", "2JA5", "" ], [ "P40422-1", "protein_xref_pdb", "2JA6", "" ], [ "P40422-1", "protein_xref_pdb", "2JA7", "" ], [ "P40422-1", "protein_xref_pdb", "2JA8", "" ], [ "P40422-1", "protein_xref_pdb", "2NVQ", "" ], [ "P40422-1", "protein_xref_pdb", "2NVT", "" ], [ "P40422-1", "protein_xref_pdb", "2NVX", "" ], [ "P40422-1", "protein_xref_pdb", "2NVY", "" ], [ "P40422-1", "protein_xref_pdb", "2NVZ", "" ], [ "P40422-1", "protein_xref_pdb", "2R7Z", "" ], [ "P40422-1", "protein_xref_pdb", "2R92", "" ], [ "P40422-1", "protein_xref_pdb", "2R93", "" ], [ "P40422-1", "protein_xref_pdb", "2VUM", "" ], [ "P40422-1", "protein_xref_pdb", "2YU9", "" ], [ "P40422-1", "protein_xref_pdb", "3CQZ", "" ], [ "P40422-1", "protein_xref_pdb", "3FKI", "" ], [ "P40422-1", "protein_xref_pdb", "3GTG", "" ], [ "P40422-1", "protein_xref_pdb", "3GTJ", "" ], [ "P40422-1", "protein_xref_pdb", "3GTK", "" ], [ "P40422-1", "protein_xref_pdb", "3GTL", "" ], [ "P40422-1", "protein_xref_pdb", "3GTM", "" ], [ "P40422-1", "protein_xref_pdb", "3GTO", "" ], [ "P40422-1", "protein_xref_pdb", "3GTP", "" ], [ "P40422-1", "protein_xref_pdb", "3GTQ", "" ], [ "P40422-1", "protein_xref_pdb", "3H3V", "" ], [ "P40422-1", "protein_xref_pdb", "3HOU", "" ], [ "P40422-1", "protein_xref_pdb", "3HOV", "" ], [ "P40422-1", "protein_xref_pdb", "3HOW", "" ], [ "P40422-1", "protein_xref_pdb", "3HOX", "" ], [ "P40422-1", "protein_xref_pdb", "3HOY", "" ], [ "P40422-1", "protein_xref_pdb", "3HOZ", "" ], [ "P40422-1", "protein_xref_pdb", "3I4M", "" ], [ "P40422-1", "protein_xref_pdb", "3I4N", "" ], [ "P40422-1", "protein_xref_pdb", "3J1N", "" ], [ "P40422-1", "protein_xref_pdb", "3K1F", "" ], [ "P40422-1", "protein_xref_pdb", "3K7A", "" ], [ "P40422-1", "protein_xref_pdb", "3M3Y", "" ], [ "P40422-1", "protein_xref_pdb", "3M4O", "" ], [ "P40422-1", "protein_xref_pdb", "3PO2", "" ], [ "P40422-1", "protein_xref_pdb", "3PO3", "" ] ] }, "readme": "Name\n - Yeast UniProtKB Xref PDB\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-08-31T13:40:29.038163\n\nModified on\n - 2023-09-11T20:29:50\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@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 Yeast UniProtKB Xref PDB contains yeast [taxid:559292] 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: uniprot-proteome-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_xref_pdb.csv\n Name: yeast_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2006\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"5629\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_xref_pdb.csv" }