{ "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": [ [ "P0DTC7-1...", "protein_xref..." ], [ "P0DTC7-1...", "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" } ], [ "P0DTC7-1", "protein_xref_pdb", "6W37", "" ], [ "P0DTC7-1", "protein_xref_pdb", "7CI3", "" ], [ "P0DTC6-1", "protein_xref_pdb", "7VPH", "" ], [ "P0DTC6-1", "protein_xref_pdb", "7F60", "" ], [ "P0DTC5-1", "protein_xref_pdb", "7VGR", "" ], [ "P0DTC5-1", "protein_xref_pdb", "7VGS", "" ], [ "P0DTC5-1", "protein_xref_pdb", "8CTK", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7K3G", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7M4R", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7NTK", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7QCS", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7TUQ", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7QCT", "" ], [ "P0DTC4-1", "protein_xref_pdb", "7QCR", "" ], [ "P0DTC3-1", "protein_xref_pdb", "6XDC", "" ], [ "P0DTC3-1", "protein_xref_pdb", "7KJR", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7EJL", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7EU2", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7F4W", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7N1A", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7N1B", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7N1E", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7N1F", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7N6D", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7N6E", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7P3D", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7P3E", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7RTD", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7RTR", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6LVN", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6LXT", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6M0J", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6M17", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6VSB", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6VXX", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6VYB", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6W41", "" ], [ "P0DTC2-1", "protein_xref_pdb", "7BH9", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6VW1", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6M1V", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6WPS", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6WPT", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6X29", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6X2A", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6X2B", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6X2C", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6X6P", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6X79", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XC2", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XC3", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XC4", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XC7", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XCM", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XCN", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XDG", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XE1", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XEY", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XF5", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XF6", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XKL", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XKP", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XKQ", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XLU", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XM0", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XM3", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XM4", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XM5", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XR8", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XRA", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6XS6", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6YZ5", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6YZ7", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6Z2M", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6Z43", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6Z97", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZB4", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZB5", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZBP", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZCZ", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZDG", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZDH", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZER", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZFO", "" ], [ "P0DTC2-1", "protein_xref_pdb", "6ZGE", "" ] ] }, "readme": "Name\n - SARS-CoV2 UniProtKB Xref PDB\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2020-04-03T12:29:53.528902\n\nModified on\n - 2022-09-26T09:05:56.490280\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]\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/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-sars-cov-2.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-sars-cov-2.nt\n Output Subdomain\n Name: sarscov2_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/sarscov2_protein_xref_pdb.csv\n Name: sarscov2_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/sarscov2_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"11\"\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: \"2650\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/sarscov2_protein_xref_pdb.csv" }