{ "bcoid": "GLY_000245", "title": "Rat UniProtKB Xref PDB", "description": "The Rat UniProtKB Xref PDB contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "Pdb cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P02761-1...", "protein_xref..." ], [ "P02761-1...", "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" } ], [ "P02761-1", "protein_xref_pdb", "2A2G", "" ], [ "P02761-1", "protein_xref_pdb", "2A2U", "" ], [ "P02767-1", "protein_xref_pdb", "1GKE", "" ], [ "P02767-1", "protein_xref_pdb", "1IE4", "" ], [ "P02767-1", "protein_xref_pdb", "1KGI", "" ], [ "P02767-1", "protein_xref_pdb", "1KGJ", "" ], [ "P02767-1", "protein_xref_pdb", "1RVS", "" ], [ "P02767-1", "protein_xref_pdb", "2M5K", "" ], [ "P02767-1", "protein_xref_pdb", "2M5M", "" ], [ "P02767-1", "protein_xref_pdb", "3ZPK", "" ], [ "A0A1W2Q641-1", "protein_xref_pdb", "6VQ6", "" ], [ "A0A1W2Q641-1", "protein_xref_pdb", "6VQ7", "" ], [ "A0A1W2Q641-1", "protein_xref_pdb", "6VQ8", "" ], [ "A0A1W2Q641-1", "protein_xref_pdb", "6VQ9", "" ], [ "A0A1W2Q641-1", "protein_xref_pdb", "6VQA", "" ], [ "A0A1W2Q641-1", "protein_xref_pdb", "6VQB", "" ], [ "Q00972-1", "protein_xref_pdb", "1GJV", "" ], [ "Q00972-1", "protein_xref_pdb", "1GKX", "" ], [ "Q00972-1", "protein_xref_pdb", "1GKZ", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ0", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ2", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ4", "" ], [ "Q00972-1", "protein_xref_pdb", "3TZ5", "" ], [ "Q00972-1", "protein_xref_pdb", "3VAD", "" ], [ "Q00972-1", "protein_xref_pdb", "4DZY", "" ], [ "Q00972-1", "protein_xref_pdb", "4E00", "" ], [ "Q00972-1", "protein_xref_pdb", "4E01", "" ], [ "Q00972-1", "protein_xref_pdb", "4E02", "" ], [ "Q00972-1", "protein_xref_pdb", "4H7Q", "" ], [ "Q00972-1", "protein_xref_pdb", "4H81", "" ], [ "Q00972-1", "protein_xref_pdb", "4H85", "" ], [ "Q00972-1", "protein_xref_pdb", "8EGD", "" ], [ "Q00972-1", "protein_xref_pdb", "8EGF", "" ], [ "Q00972-1", "protein_xref_pdb", "8EGQ", "" ], [ "Q00972-1", "protein_xref_pdb", "8EGU", "" ], [ "P31016-1", "protein_xref_pdb", "3WP0", "" ], [ "P31016-1", "protein_xref_pdb", "3WP1", "" ], [ "P31016-1", "protein_xref_pdb", "5GNV", "" ], [ "P31016-1", "protein_xref_pdb", "5B64", "" ], [ "P31016-1", "protein_xref_pdb", "5YPO", "" ], [ "P31016-1", "protein_xref_pdb", "1BE9", "" ], [ "P31016-1", "protein_xref_pdb", "1BFE", "" ], [ "P31016-1", "protein_xref_pdb", "1IU0", "" ], [ "P31016-1", "protein_xref_pdb", "1IU2", "" ], [ "P31016-1", "protein_xref_pdb", "1JXM", "" ], [ "P31016-1", "protein_xref_pdb", "1JXO", "" ], [ "P31016-1", "protein_xref_pdb", "1KJW", "" ], [ "P31016-1", "protein_xref_pdb", "1QLC", "" ], [ "P31016-1", "protein_xref_pdb", "1RGR", "" ], [ "P31016-1", "protein_xref_pdb", "1TP3", "" ], [ "P31016-1", "protein_xref_pdb", "1TP5", "" ], [ "P31016-1", "protein_xref_pdb", "1TQ3", "" ], [ "P31016-1", "protein_xref_pdb", "2KA9", "" ], [ "P31016-1", "protein_xref_pdb", "2MHO", "" ], [ "P31016-1", "protein_xref_pdb", "3GSL", "" ], [ "P31016-1", "protein_xref_pdb", "5D13", "" ], [ "P31016-1", "protein_xref_pdb", "5HDY", "" ], [ "P31016-1", "protein_xref_pdb", "5HEB", "" ], [ "P31016-1", "protein_xref_pdb", "5HED", "" ], [ "P31016-1", "protein_xref_pdb", "5HET", "" ], [ "P31016-1", "protein_xref_pdb", "5HEY", "" ], [ "P31016-1", "protein_xref_pdb", "5HF1", "" ], [ "P31016-1", "protein_xref_pdb", "5HF4", "" ], [ "P31016-1", "protein_xref_pdb", "5HFB", "" ], [ "P31016-1", "protein_xref_pdb", "5HFC", "" ], [ "P31016-1", "protein_xref_pdb", "5HFD", "" ], [ "P31016-1", "protein_xref_pdb", "5HFE", "" ], [ "P31016-1", "protein_xref_pdb", "5HFF", "" ], [ "P31016-1", "protein_xref_pdb", "5MZ7", "" ], [ "P31016-1", "protein_xref_pdb", "5W72", "" ], [ "P31016-1", "protein_xref_pdb", "5YPR", "" ], [ "P31016-1", "protein_xref_pdb", "7CQF", "" ], [ "P31016-1", "protein_xref_pdb", "7F7G", "" ], [ "P31016-1", "protein_xref_pdb", "7F7I", "" ], [ "B1WBP0-1", "protein_xref_pdb", "3RL3", "" ], [ "B1WBP0-1", "protein_xref_pdb", "3RL4", "" ], [ "B1WBP0-1", "protein_xref_pdb", "3RL5", "" ], [ "Q62735-1", "protein_xref_pdb", "1OSV", "" ], [ "Q62735-1", "protein_xref_pdb", "1OT7", "" ], [ "O35923-1", "protein_xref_pdb", "1IYJ", "" ], [ "B0BN93-1", "protein_xref_pdb", "6EPC", "" ], [ "B0BN93-1", "protein_xref_pdb", "6EPD", "" ], [ "B0BN93-1", "protein_xref_pdb", "6EPE", "" ], [ "B0BN93-1", "protein_xref_pdb", "6EPF", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref PDB\n\nVersion\n - v-2.3.1\n\nCreated on\n - 2019-09-06T14:06:38.971888\n\nModified on\n - 2022-09-26T09:04:47.896933\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 Rat UniProtKB Xref PDB contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to PDB database accessions/identifiers. The dataset is derived from 2019-09 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-rattus-norvegicus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_protein_xref_pdb.csv\n Name: rat_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/rat_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"729\"\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: \"3802\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/rat_protein_xref_pdb.csv" }