{ "bcoid": "GLY_000916", "title": "Pig UniProtKB Xref PDB", "description": "The Pig UniProtKB Xref PDB contains pig [taxid:9823] UniProtKB canonical accessions cross-referenced ...", "filename": "pig_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": [ "Sus scrofa" ], "molecule": [ "Protein" ], "tag": [ "Pdb cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "F1S1A8-1...", "protein_xref..." ], [ "F1S1A8-1...", "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" } ], [ "F1S1A8-1", "protein_xref_pdb", "7VYE", "" ], [ "F1S1A8-1", "protein_xref_pdb", "7VZ8", "" ], [ "P00889-1", "protein_xref_pdb", "1CTS", "" ], [ "P00889-1", "protein_xref_pdb", "2CTS", "" ], [ "P00889-1", "protein_xref_pdb", "3ENJ", "" ], [ "P00889-1", "protein_xref_pdb", "4CTS", "" ], [ "P00889-1", "protein_xref_pdb", "5UQS", "" ], [ "A0A287AWH6-1", "protein_xref_pdb", "7V2C", "" ], [ "A0A287AWH6-1", "protein_xref_pdb", "7V2E", "" ], [ "P16293-1", "protein_xref_pdb", "1PFX", "" ], [ "P16293-1", "protein_xref_pdb", "1X7A", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "5GPN", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "5GUP", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2C", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2D", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2E", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2F", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2H", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2K", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V2R", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V30", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V31", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V32", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V33", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7V3M", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VB7", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VBN", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VBZ", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VWJ", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VXP", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VY8", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VYA", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VYF", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VYH", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VYN", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VZ1", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VZV", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7VZW", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W00", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W0H", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W0R", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W0Y", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W1O", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W1P", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W1T", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W1U", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W1V", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W1Z", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W20", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W2K", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W2L", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W2R", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W2U", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W2Y", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W31", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W32", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W35", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4C", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4D", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4E", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4F", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4G", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4J", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4K", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4L", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4M", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4N", "" ], [ "A0A5G2R526-1", "protein_xref_pdb", "7W4Q", "" ], [ "P63053-1", "protein_xref_pdb", "3J7O", "" ], [ "P63053-1", "protein_xref_pdb", "3J7P", "" ], [ "P63053-1", "protein_xref_pdb", "3J7Q", "" ], [ "P63053-1", "protein_xref_pdb", "3J7R", "" ], [ "K9IWA3-1", "protein_xref_pdb", "7U8O", "" ], [ "K9IWA3-1", "protein_xref_pdb", "7U8P", "" ], [ "K9IWA3-1", "protein_xref_pdb", "7U8Q", "" ], [ "K9IWA3-1", "protein_xref_pdb", "7U8R", "" ], [ "F1SR64-1", "protein_xref_pdb", "7NSH", "" ], [ "F1SR64-1", "protein_xref_pdb", "6GAW", "" ], [ "F1SR64-1", "protein_xref_pdb", "6GB2", "" ], [ "F1SR64-1", "protein_xref_pdb", "6YDP", "" ], [ "F1SR64-1", "protein_xref_pdb", "6YDW", "" ], [ "F1SR64-1", "protein_xref_pdb", "7NSI", "" ], [ "F1SR64-1", "protein_xref_pdb", "7NQH", "" ], [ "F1SR64-1", "protein_xref_pdb", "7NQL", "" ] ] }, "readme": "Name\n - Pig UniProtKB Xref PDB\n\nVersion\n - v-2.4.1\n\nCreated on\n - \n\nModified on\n - \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], 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 Pig UniProtKB Xref PDB contains pig [taxid:9823] 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-sus_scrofa.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_13/uniprot-proteome-sus_scrofa.nt\n Output Subdomain\n Name: pig_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_xref_pdb.csv\n Name: pig_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"399\"\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: \"1291\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/pig_protein_xref_pdb.csv" }