{ "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", "" ], [ "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", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2A5K", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2ACF", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2AHM", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2AJ5", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2ALV", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2AMD", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2AMQ", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2BX3", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2BX4", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2C3S", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2D2D", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2DUC", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2FAV", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2FE8", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2FYG", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2G9T", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GA6", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GDT", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GRI", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GT7", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GT8", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GTB", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GX4", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GZ7", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GZ8", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2GZ9", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2H2Z", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2HOB", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2HSX", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2IDY", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2KAF", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2KQV", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2KQW", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2KYS", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2LIZ", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2OP9", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2PWX", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2W2G", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2WCT", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2Z3C", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2Z3D", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2Z3E", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2ZU4", "" ], [ "P0C6U8-1", "protein_xref_pdb", "2ZU5", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3ATW", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3AVZ", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3AW0", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3AW1", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3E91", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3EA7", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3EA8", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3EA9", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3EAJ", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3EE7", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3F9E", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3F9F", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3F9G", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3F9H", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3FZD", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3IWM", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3M3S", "" ], [ "P0C6U8-1", "protein_xref_pdb", "3M3T", "" ] ] }, "readme": "Name\n - SARS-CoV1 UniProtKB Xref PDB\n\nVersion\n - 1.8.25\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]\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: uniprot-proteome-694009-human-sars-coronavirus-2019-05.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/uniprot-proteome-694009-human-sars-coronavirus-2019-05.nt\n Name: sarscov1_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov1_protein_masterlist.csv\n Output Subdomain\n Name: sarscov1_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov1_protein_xref_pdb.csv\n Name: sarscov1_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov1_protein_xref_pdb.stat.csv\n\nFields\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"\n Name: \"title\"\n Description: \"Title of the published article in the journal\"\n Unique Values: \"119\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"120\"\n Name: \"journal_name\"\n Description: \"The name of the journal in which the article is published\"\n Unique Values: \"49\"\n Name: \"authors\"\n Description: \"NA\"\n Unique Values: \"118\"\n Name: \"publication_date\"\n Description: \"Contains the full date on which the issue of the journal was published. Sourced from MEDLINE/PubMed data element(fields) description.\"\n Unique Values: \"117\"\n Name: \"glytoucan_ac\"\n Description: \"Unique accession assigned to the registered glycan structure in GlyTouCan database\"\n Unique Values: \"115\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.8.25/reviewed/sarscov1_protein_xref_pdb.csv" }