{ "bcoid": "GLY_000452", "title": "SARS-CoV2 UniProtKB Xref PDB", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCov) UniProtKB Xref PDB contains sarscov2 [taxid:2697049] UniProtKB ...", "filename": "sarscov2_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "Pdb cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD2-1...", "protein_xref..." ], [ "P0DTD2-1...", "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" } ], [ "P0DTD2-1", "protein_xref_pdb", "6Z4U", "" ], [ "P0DTD2-1", "protein_xref_pdb", "7KDT", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6LU7", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R7Y", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R7Z", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R80", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R81", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R82", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R83", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5R84", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RE4", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RE5", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RE6", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RE7", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RE8", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RE9", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REA", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REB", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REC", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RED", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REE", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REF", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REG", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REH", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REI", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REJ", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REK", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REL", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REM", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REN", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REO", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REP", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RER", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RES", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RET", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REU", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REV", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REW", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REX", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REY", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5REZ", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF0", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF1", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF2", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF3", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF4", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF5", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF6", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF7", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF8", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RF9", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFA", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFB", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFC", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFD", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFE", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFF", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFG", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFH", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFI", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFJ", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFK", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFL", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFM", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFN", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFO", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFP", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFQ", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFR", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFS", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFT", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFU", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFV", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFW", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFX", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFY", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RFZ", "" ], [ "P0DTD1-1", "protein_xref_pdb", "5RG0", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6M03", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6VWW", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6W01", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6W02", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6W61", "" ], [ "P0DTD1-1", "protein_xref_pdb", "6W63", "" ] ] }, "readme": "Name\n - SARS-CoV2 UniProtKB Xref PDB\n\nVersion\n - 1.8.25\n\nCreated on\n - 2020-04-03T12:29:53.528902\n\nModified on\n - 2021-02-22T17:21:40.888720\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-2 or 2019-nCov) UniProtKB Xref PDB contains sarscov2 [taxid:2697049] 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-2697049-human-sars-coronavirus-2019-05.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/source/uniprot-proteome-2697049-human-sars-coronavirus-2019-05.nt\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_protein_masterlist.csv\n Output Subdomain\n Name: sarscov2_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_protein_xref_pdb.csv\n Name: sarscov2_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.8.25/reviewed/sarscov2_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/sarscov2_protein_xref_pdb.csv" }