{ "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": [ [ "Q8TBF4-1...", "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" } ], [ "Q8TBF4-1", "protein_xref_pdb", "2E5H", "" ], [ "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", "" ], [ "Q9NQ75-1", "protein_xref_pdb", "2CRE", "" ], [ "P20930-1", "protein_xref_pdb", "4PCW", "" ], [ "P20933-1", "protein_xref_pdb", "1APY", "" ], [ "P20933-1", "protein_xref_pdb", "1APZ", "" ], [ "P20936-1", "protein_xref_pdb", "1WER", "" ], [ "P20936-1", "protein_xref_pdb", "1WQ1", "" ], [ "P20936-1", "protein_xref_pdb", "2GQI", "" ], [ "P20936-1", "protein_xref_pdb", "2GSB", "" ], [ "P20936-1", "protein_xref_pdb", "2J05", "" ], [ "P20936-1", "protein_xref_pdb", "2J06", "" ], [ "P20936-1", "protein_xref_pdb", "2M51", "" ], [ "P20936-1", "protein_xref_pdb", "4FSS", "" ], [ "Q9H999-1", "protein_xref_pdb", "2I7P", "" ], [ "Q9H999-1", "protein_xref_pdb", "3MK6", "" ], [ "Q9H999-1", "protein_xref_pdb", "3SMS", "" ], [ "Q9H999-1", "protein_xref_pdb", "5KPR", "" ], [ "Q9H999-1", "protein_xref_pdb", "5KPT", "" ], [ "Q9H999-1", "protein_xref_pdb", "5KPZ", "" ], [ "Q9H999-1", "protein_xref_pdb", "5KQ8", "" ], [ "Q9H999-1", "protein_xref_pdb", "5KQD", "" ], [ "Q9H999-1", "protein_xref_pdb", "6B3V", "" ], [ "P23919-1", "protein_xref_pdb", "1E2D", "" ], [ "P23919-1", "protein_xref_pdb", "1E2E", "" ], [ "P23919-1", "protein_xref_pdb", "1E2F", "" ], [ "P23919-1", "protein_xref_pdb", "1E2G", "" ], [ "P23919-1", "protein_xref_pdb", "1E2Q", "" ], [ "P23919-1", "protein_xref_pdb", "1E98", "" ], [ "P23919-1", "protein_xref_pdb", "1E99", "" ], [ "P23919-1", "protein_xref_pdb", "1E9A", "" ], [ "P23919-1", "protein_xref_pdb", "1E9B", "" ], [ "P23919-1", "protein_xref_pdb", "1E9C", "" ], [ "P23919-1", "protein_xref_pdb", "1E9D", "" ], [ "P23919-1", "protein_xref_pdb", "1E9E", "" ], [ "P23919-1", "protein_xref_pdb", "1E9F", "" ], [ "P23919-1", "protein_xref_pdb", "1NMX", "" ], [ "P23919-1", "protein_xref_pdb", "1NMY", "" ], [ "P23919-1", "protein_xref_pdb", "1NMZ", "" ], [ "P23919-1", "protein_xref_pdb", "1NN0", "" ], [ "P23919-1", "protein_xref_pdb", "1NN1", "" ], [ "P23919-1", "protein_xref_pdb", "1NN3", "" ], [ "P23919-1", "protein_xref_pdb", "1NN5", "" ], [ "P23919-1", "protein_xref_pdb", "2XX3", "" ], [ "Q8NHX9-1", "protein_xref_pdb", "6NQ0", "" ], [ "Q8NHX9-1", "protein_xref_pdb", "6NQ1", "" ], [ "Q8NHX9-1", "protein_xref_pdb", "6NQ2", "" ], [ "Q9NXR8-1", "protein_xref_pdb", "1X4I", "" ], [ "Q00536-1", "protein_xref_pdb", "3MTL", "" ], [ "Q00536-1", "protein_xref_pdb", "5G6V", "" ], [ "Q00532-1", "protein_xref_pdb", "4AGU", "" ], [ "O00244-1", "protein_xref_pdb", "2K1R", "" ], [ "O00244-1", "protein_xref_pdb", "3CJK", "" ], [ "O00244-1", "protein_xref_pdb", "5T7L", "" ], [ "O00244-1", "protein_xref_pdb", "1FE0", "" ], [ "O00244-1", "protein_xref_pdb", "1FE4", "" ], [ "O00244-1", "protein_xref_pdb", "1FEE", "" ], [ "O00244-1", "protein_xref_pdb", "1TL4", "" ], [ "O00244-1", "protein_xref_pdb", "1TL5", "" ], [ "O00244-1", "protein_xref_pdb", "2LQ9", "" ], [ "O00244-1", "protein_xref_pdb", "3IWL", "" ], [ "O00244-1", "protein_xref_pdb", "3IWX", "" ], [ "O00244-1", "protein_xref_pdb", "4QOT", "" ], [ "O00244-1", "protein_xref_pdb", "4YDX", "" ], [ "O00244-1", "protein_xref_pdb", "4YEA", "" ], [ "O00244-1", "protein_xref_pdb", "5F0W", "" ], [ "O00241-1", "protein_xref_pdb", "2D9C", "" ], [ "O00241-1", "protein_xref_pdb", "2JJU", "" ], [ "Q8IX01-1", "protein_xref_pdb", "1X4P", "" ], [ "P24522-1", "protein_xref_pdb", "2KG4", "" ], [ "Q13835-1", "protein_xref_pdb", "1XM9", "" ], [ "P40424-1", "protein_xref_pdb", "1PUF", "" ], [ "P40424-1", "protein_xref_pdb", "1B72", "" ], [ "Q8IZK6-1", "protein_xref_pdb", "6HRR", "" ], [ "Q8IZK6-1", "protein_xref_pdb", "6HRS", "" ] ] }, "readme": "Name\n - Human UniProtKB Xref PDB\n\nVersion\n - 1.7.10\n\nCreated on\n - 2019-03-15T15:08:57.534471\n\nModified on\n - 2020-04-10T11:38:26.443842\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]\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/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-9606-homo-sapiens-2019-05.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.7.10/source/uniprot-proteome-9606-homo-sapiens-2019-05.nt\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/human_protein_xref_pdb.csv\n Name: human_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.7.10/reviewed/human_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"6731\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"43817\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.7.10/reviewed/human_protein_xref_pdb.csv" }