{ "bcoid": "GLY_000120", "title": "Mouse UniProtKB Xref PDB", "description": "The Mouse UniProtKB Xref PDB contains mouse [taxid:10090] UniProtKB canonical accessions cross-referenced ...", "filename": "mouse_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": "Mus Musculus", "molecule": "Protein", "tags": "Pdb cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P01942-1...", "3HRW..." ], [ "P03899-1...", "6G2J..." ] ], "headers": [ "uniprotkb_ca...", "database_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "database_label" } ], [ "P01942-1", "3HRW", "" ], [ "P03899-1", "6G2J", "" ], [ "P03899-1", "6G72", "" ], [ "P03893-1", "6G2J", "" ], [ "P03893-1", "6G72", "" ], [ "P02762-1", "2NND", "" ], [ "P02762-1", "2NNE", "" ], [ "P02762-1", "1I04", "" ], [ "P02762-1", "1I05", "" ], [ "P02762-1", "1I06", "" ], [ "P02762-1", "1MUP", "" ], [ "P02762-1", "2LB6", "" ], [ "Q5EBH1-1", "1RFH", "" ], [ "Q5EBH1-1", "2FNF", "" ], [ "Q5EBH1-1", "2YMY", "" ], [ "Q5EBH1-1", "3DDC", "" ], [ "O08912-1", "1XHB", "" ], [ "Q66GT5-1", "3RGO", "" ], [ "Q66GT5-1", "3RGQ", "" ], [ "Q7M729-1", "5AYQ", "" ], [ "Q7M729-1", "5XAX", "" ], [ "P10648-1", "1ML6", "" ], [ "Q9DB00-1", "1UG2", "" ], [ "Q6PDM2-1", "1X4C", "" ], [ "Q9QUN7-1", "2Z81", "" ], [ "Q9QUN7-1", "2Z82", "" ], [ "Q9QUN7-1", "3A79", "" ], [ "Q9QUN7-1", "3A7B", "" ], [ "Q9QUN7-1", "3A7C", "" ], [ "Q9QUN7-1", "5D3I", "" ], [ "Q9QUN3-1", "2EO6", "" ], [ "Q91Z69-1", "2GNC", "" ], [ "O70274-1", "5K24", "" ], [ "Q69Z98-1", "4YNZ", "" ], [ "Q69Z98-1", "4YOM", "" ], [ "Q5NCY0-1", "4EZH", "" ], [ "Q5NCY0-1", "4EYU", "" ], [ "Q5NCY0-1", "4EZ4", "" ], [ "Q9ESN9-1", "6EJN", "" ], [ "Q9ESN4-1", "5YBZ", "" ], [ "Q9ESN4-1", "4QQH", "" ], [ "Q9ESN4-1", "4QQL", "" ], [ "Q9ESN4-1", "4QQO", "" ], [ "Q9ESN4-1", "4QQP", "" ], [ "Q91XE4-1", "3NFZ", "" ], [ "Q91XE4-1", "3NH4", "" ], [ "Q91XE4-1", "3NH5", "" ], [ "Q91XE4-1", "3NH8", "" ], [ "P00520-1", "1ABO", "" ], [ "P00520-1", "1ABQ", "" ], [ "P00520-1", "1FPU", "" ], [ "P00520-1", "1IEP", "" ], [ "P00520-1", "1OPJ", "" ], [ "P00520-1", "2QOH", "" ], [ "P00520-1", "2Z60", "" ], [ "P00520-1", "3DK3", "" ], [ "P00520-1", "3DK6", "" ], [ "P00520-1", "3DK7", "" ], [ "P00520-1", "3IK3", "" ], [ "P00520-1", "3K5V", "" ], [ "P00520-1", "3KF4", "" ], [ "P00520-1", "3MS9", "" ], [ "P00520-1", "3MSS", "" ], [ "P00520-1", "3OXZ", "" ], [ "P00520-1", "3OY3", "" ], [ "P00520-1", "5IH2", "" ], [ "P00520-1", "1M52", "" ], [ "P00520-1", "1OPK", "" ], [ "P00520-1", "2HZN", "" ], [ "P00520-1", "3KFA", "" ], [ "P00520-1", "6HD4", "" ], [ "P00520-1", "6HD6", "" ], [ "Q923B0-1", "1VKB", "" ], [ "Q923B0-1", "2KL2", "" ], [ "Q8C0V1-1", "1X58", "" ], [ "Q9R002-1", "4JBJ", "" ], [ "Q9R002-1", "4JBK", "" ], [ "Q9R002-1", "4L5Q", "" ], [ "Q9R002-1", "4L5R", "" ], [ "Q9R002-1", "4L5S", "" ], [ "Q9R002-1", "4L5T", "" ], [ "Q9R002-1", "4LNQ", "" ], [ "O70133-1", "1UIL", "" ], [ "O70133-1", "1WHQ", "" ] ] }, "readme": "Name\n - Mouse UniProtKB Xref PDB\n\nVersion\n - 1.5.11\n\nCreated on\n - 2019-03-15T15:11:39.076274\n\nModified on\n - 2019-11-27T14:47:25.023665\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 Mouse UniProtKB Xref PDB contains mouse [taxid:10090] 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-mus-musculus.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-mus-musculus.nt\n Name: mouse_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_masterlist.csv\n Output Subdomain\n Name: mouse_protein_xref_pdb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_pdb.csv\n Name: mouse_protein_xref_pdb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/mouse_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"1880\"\n Name: \"database_label\"\n Description: \"Label or name assigned to the corresponding identifier in the source database\"\n Unique Values: \"1\"\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"5326\"", "downloadurl": "/ln2data/releases/data/v-1.5.11/reviewed/mouse_protein_xref_pdb.csv" }