{ "bcoid": "GLY_000119", "title": "Human UniProtKB Xref PDB", "description": "The Human UniProtKB Xref PDB contains human [taxid:9606] UniProtKB canonical accessions cross-referenced ...", "filename": "human_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Pdb cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P30613-1...", "protein_xref..." ], [ "P30613-1...", "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" } ], [ "P30613-1", "protein_xref_pdb", "2VGB", "" ], [ "P30613-1", "protein_xref_pdb", "2VGF", "" ], [ "P30613-1", "protein_xref_pdb", "2VGG", "" ], [ "P30613-1", "protein_xref_pdb", "2VGI", "" ], [ "P30613-1", "protein_xref_pdb", "4IMA", "" ], [ "P30613-1", "protein_xref_pdb", "4IP7", "" ], [ "P30613-1", "protein_xref_pdb", "6NN4", "" ], [ "P30613-1", "protein_xref_pdb", "6NN5", "" ], [ "P30613-1", "protein_xref_pdb", "6NN7", "" ], [ "P30613-1", "protein_xref_pdb", "6NN8", "" ], [ "P30613-1", "protein_xref_pdb", "7QDN", "" ], [ "P40424-1", "protein_xref_pdb", "1PUF", "" ], [ "P40424-1", "protein_xref_pdb", "1B72", "" ], [ "P40429-1", "protein_xref_pdb", "4V6X", "" ], [ "P40429-1", "protein_xref_pdb", "4UG0", "" ], [ "P40429-1", "protein_xref_pdb", "5AJ0", "" ], [ "P40429-1", "protein_xref_pdb", "5LKS", "" ], [ "P40429-1", "protein_xref_pdb", "5T2C", "" ], [ "P40429-1", "protein_xref_pdb", "6QZP", "" ], [ "P40429-1", "protein_xref_pdb", "6IP5", "" ], [ "P40429-1", "protein_xref_pdb", "6IP6", "" ], [ "P40429-1", "protein_xref_pdb", "6IP8", "" ], [ "P40429-1", "protein_xref_pdb", "6OLE", "" ], [ "P40429-1", "protein_xref_pdb", "6OLF", "" ], [ "P40429-1", "protein_xref_pdb", "6OLG", "" ], [ "P40429-1", "protein_xref_pdb", "6OLI", "" ], [ "P40429-1", "protein_xref_pdb", "6OLZ", "" ], [ "P40429-1", "protein_xref_pdb", "6OM0", "" ], [ "P40429-1", "protein_xref_pdb", "6OM7", "" ], [ "P40429-1", "protein_xref_pdb", "6XA1", "" ], [ "P40429-1", "protein_xref_pdb", "7BHP", "" ], [ "P40429-1", "protein_xref_pdb", "6W6L", "" ], [ "P40429-1", "protein_xref_pdb", "6LQM", "" ], [ "P40429-1", "protein_xref_pdb", "6LSR", "" ], [ "P40429-1", "protein_xref_pdb", "6LSS", "" ], [ "P40429-1", "protein_xref_pdb", "6LU8", "" ], [ "P40429-1", "protein_xref_pdb", "6Y6X", "" ], [ "P40429-1", "protein_xref_pdb", "6Y0G", "" ], [ "P40429-1", "protein_xref_pdb", "6Y2L", "" ], [ "P40429-1", "protein_xref_pdb", "6Y57", "" ], [ "P40429-1", "protein_xref_pdb", "6Z6L", "" ], [ "P40429-1", "protein_xref_pdb", "6Z6M", "" ], [ "P40429-1", "protein_xref_pdb", "6Z6N", "" ], [ "P40429-1", "protein_xref_pdb", "6ZM7", "" ], [ "P40429-1", "protein_xref_pdb", "6ZME", "" ], [ "P40429-1", "protein_xref_pdb", "6ZMI", "" ], [ "P40429-1", "protein_xref_pdb", "6ZMO", "" ], [ "P40429-1", "protein_xref_pdb", "7F5S", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "5XJC", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "2HYI", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "2J0Q", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "2J0S", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "2XB2", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "3EX7", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "1P27", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "5YZG", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "6ICZ", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "6QDV", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "7A5P", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "7W59", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "7W5A", "" ], [ "Q9Y5S9-1", "protein_xref_pdb", "7W5B", "" ], [ "Q96RU3-1", "protein_xref_pdb", "2EFL", "" ], [ "Q96RU2-1", "protein_xref_pdb", "2LVA", "" ], [ "Q96RU2-1", "protein_xref_pdb", "2MUU", "" ], [ "Q96RU2-1", "protein_xref_pdb", "6H4I", "" ], [ "Q96RU2-1", "protein_xref_pdb", "6HEH", "" ], [ "Q96RU2-1", "protein_xref_pdb", "6HEJ", "" ], [ "Q96RU2-1", "protein_xref_pdb", "6H4H", "" ], [ "Q96RU2-1", "protein_xref_pdb", "6HEI", "" ], [ "Q96RU2-1", "protein_xref_pdb", "6HEK", "" ], [ "Q96RU8-1", "protein_xref_pdb", "5CEK", "" ], [ "Q96RU8-1", "protein_xref_pdb", "5CEM", "" ], [ "Q96RU8-1", "protein_xref_pdb", "5IGO", "" ], [ "Q96RU8-1", "protein_xref_pdb", "5IGQ", "" ], [ "Q96RU8-1", "protein_xref_pdb", "6DC0", "" ], [ "Q8NCJ5-1", "protein_xref_pdb", "2YYO", "" ], [ "Q9Y296-1", "protein_xref_pdb", "2J3T", "" ], [ "Q9Y296-1", "protein_xref_pdb", "2JSN", "" ], [ "Q9Y296-1", "protein_xref_pdb", "2ZMV", "" ], [ "Q9Y297-1", "protein_xref_pdb", "1P22", "" ], [ "Q9Y297-1", "protein_xref_pdb", "2P64", "" ], [ "Q9Y297-1", "protein_xref_pdb", "6M90", "" ], [ "Q9Y297-1", "protein_xref_pdb", "6M91", "" ] ] }, "readme": "Name\n - Human UniProtKB Xref PDB\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2019-03-15T15:08:57.534471\n\nModified on\n - 2022-09-26T08:56:48.512043\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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 Human UniProtKB Xref PDB contains human [taxid:9606] 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-homo-sapiens.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-homo-sapiens.nt\n Output Subdomain\n Name: human_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_xref_pdb.csv\n Name: human_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/human_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"7712\"\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: \"55521\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/human_protein_xref_pdb.csv" }