{ "bcoid": "GLY_000451", "title": "SARS-CoV1 UniProtKB Xref PDB", "description": "The SARS coronavirus (SARS-CoV-1) UniProtKB Xref PDB contains sarscov1 [taxid:694009] UniProtKB canonical ...", "filename": "sarscov1_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-1)", "molecule": "Protein", "tags": "Pdb cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P59596-1...", "protein_xref..." ], [ "P59596-1...", "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" } ], [ "P59596-1", "protein_xref_pdb", "3I6G", "" ], [ "P59596-1", "protein_xref_pdb", "3I6K", "" ], [ "P59596-1", "protein_xref_pdb", "3TO2", "" ], [ "P59594-1", "protein_xref_pdb", "6CS2", "" ], [ "P59594-1", "protein_xref_pdb", "1XJP", "" ], [ "P59594-1", "protein_xref_pdb", "2AJF", "" ], [ "P59594-1", "protein_xref_pdb", "3D0G", "" ], [ "P59594-1", "protein_xref_pdb", "3D0H", "" ], [ "P59594-1", "protein_xref_pdb", "3D0I", "" ], [ "P59594-1", "protein_xref_pdb", "3SCI", "" ], [ "P59594-1", "protein_xref_pdb", "3SCJ", "" ], [ "P59594-1", "protein_xref_pdb", "3SCK", "" ], [ "P59594-1", "protein_xref_pdb", "3SCL", "" ], [ "P59594-1", "protein_xref_pdb", "3BGF", "" ], [ "P59594-1", "protein_xref_pdb", "6ACG", "" ], [ "P59594-1", "protein_xref_pdb", "6ACJ", "" ], [ "P59594-1", "protein_xref_pdb", "6ACK", "" ], [ "P59594-1", "protein_xref_pdb", "1Q4Z", "" ], [ "P59594-1", "protein_xref_pdb", "1T7G", "" ], [ "P59594-1", "protein_xref_pdb", "1U4K", "" ], [ "P59594-1", "protein_xref_pdb", "1WNC", "" ], [ "P59594-1", "protein_xref_pdb", "1WYY", "" ], [ "P59594-1", "protein_xref_pdb", "1ZV7", "" ], [ "P59594-1", "protein_xref_pdb", "1ZV8", "" ], [ "P59594-1", "protein_xref_pdb", "1ZVB", "" ], [ "P59594-1", "protein_xref_pdb", "2BEQ", "" ], [ "P59594-1", "protein_xref_pdb", "2BEZ", "" ], [ "P59594-1", "protein_xref_pdb", "2DD8", "" ], [ "P59594-1", "protein_xref_pdb", "2FXP", "" ], [ "P59594-1", "protein_xref_pdb", "2GHV", "" ], [ "P59594-1", "protein_xref_pdb", "2GHW", "" ], [ "P59594-1", "protein_xref_pdb", "2RUM", "" ], [ "P59594-1", "protein_xref_pdb", "2RUN", "" ], [ "P59594-1", "protein_xref_pdb", "2RUO", "" ], [ "P59594-1", "protein_xref_pdb", "5WRG", "" ], [ "P59594-1", "protein_xref_pdb", "5X4S", "" ], [ "P59594-1", "protein_xref_pdb", "5X58", "" ], [ "P59594-1", "protein_xref_pdb", "5X5B", "" ], [ "P59594-1", "protein_xref_pdb", "5XJK", "" ], [ "P59594-1", "protein_xref_pdb", "5XLR", "" ], [ "P59594-1", "protein_xref_pdb", "5ZVM", "" ], [ "P59594-1", "protein_xref_pdb", "6ACC", "" ], [ "P59594-1", "protein_xref_pdb", "6ACD", "" ], [ "P59594-1", "protein_xref_pdb", "6CRV", "" ], [ "P59594-1", "protein_xref_pdb", "6CRW", "" ], [ "P59594-1", "protein_xref_pdb", "6CRX", "" ], [ "P59594-1", "protein_xref_pdb", "6CRZ", "" ], [ "P59594-1", "protein_xref_pdb", "6CS0", "" ], [ "P59594-1", "protein_xref_pdb", "6CS1", "" ], [ "P59594-1", "protein_xref_pdb", "6NB6", "" ], [ "P59594-1", "protein_xref_pdb", "6NB7", "" ], [ "P59594-1", "protein_xref_pdb", "6VW1", "" ], [ "P59594-1", "protein_xref_pdb", "6M3W", "" ], [ "P59594-1", "protein_xref_pdb", "6WAQ", "" ], [ "P59594-1", "protein_xref_pdb", "7JN5", "" ], [ "P59595-1", "protein_xref_pdb", "3I6L", "" ], [ "P59595-1", "protein_xref_pdb", "1X7Q", "" ], [ "P59595-1", "protein_xref_pdb", "1SSK", "" ], [ "P59595-1", "protein_xref_pdb", "2CJR", "" ], [ "P59595-1", "protein_xref_pdb", "2GIB", "" ], [ "P59595-1", "protein_xref_pdb", "2JW8", "" ], [ "P59595-1", "protein_xref_pdb", "2OFZ", "" ], [ "P59595-1", "protein_xref_pdb", "2OG3", "" ], [ "P59595-1", "protein_xref_pdb", "7LG0", "" ], [ "P59595-1", "protein_xref_pdb", "6IEX", "" ], [ "P0C6U8-1", "protein_xref_pdb", "4MM3", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1P76", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1P9T", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1PA5", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1PUK", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1Q1X", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1Q2W", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1QZ8", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1UJ1", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1UK2", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1UK3", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1UK4", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1UW7", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1WOF", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1YSY", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1Z1I", "" ], [ "P0C6U8-1", "protein_xref_pdb", "1Z1J", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2A5A", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2A5I", "" ] ] }, "readme": "Name\n - SARS-CoV1 UniProtKB Xref PDB\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-04-03T12:28:56.594146\n\nModified on\n - 2020-04-09T18:52:57.173557\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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 SARS coronavirus (SARS-CoV-1) UniProtKB Xref PDB contains sarscov1 [taxid:694009] UniProtKB canonical accessions cross-referenced to PDB database accessions/identifiers. The dataset is derived from 2020-01 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: sarscov1_protein_masterlist.csv\n URI: https://data.glygen.org//ln2releases/data/v-1.11.2/reviewed/sarscov1_protein_masterlist.csv\n Name: uniprot-proteome-694009-human-sars-coronavirus-2019-05.nt\n URI: https://data.glygen.org//ln2downloads/ebi/2021_03/uniprot-proteome-sars-coronavirus.nt\n Output Subdomain\n Name: sarscov1_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov1_protein_xref_pdb.csv\n Name: sarscov1_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov1_protein_xref_pdb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/sarscov1_protein_xref_pdb.csv" }