{ "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": [ [ "P03899-1...", "protein_xref..." ], [ "P03899-1...", "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" } ], [ "P03899-1", "protein_xref_pdb", "6G2J", "" ], [ "P03899-1", "protein_xref_pdb", "6G72", "" ], [ "P03899-1", "protein_xref_pdb", "6ZR2", "" ], [ "P03899-1", "protein_xref_pdb", "6ZTQ", "" ], [ "P03899-1", "protein_xref_pdb", "7AK5", "" ], [ "P03899-1", "protein_xref_pdb", "7AK6", "" ], [ "P03899-1", "protein_xref_pdb", "7B93", "" ], [ "P03899-1", "protein_xref_pdb", "7PSA", "" ], [ "P03893-1", "protein_xref_pdb", "6G2J", "" ], [ "P03893-1", "protein_xref_pdb", "6G72", "" ], [ "P03893-1", "protein_xref_pdb", "6ZR2", "" ], [ "P03893-1", "protein_xref_pdb", "6ZTQ", "" ], [ "P03893-1", "protein_xref_pdb", "7AK5", "" ], [ "P03893-1", "protein_xref_pdb", "7AK6", "" ], [ "P03893-1", "protein_xref_pdb", "7B93", "" ], [ "P03893-1", "protein_xref_pdb", "7PSA", "" ], [ "P02762-1", "protein_xref_pdb", "2NND", "" ], [ "P02762-1", "protein_xref_pdb", "2NNE", "" ], [ "P02762-1", "protein_xref_pdb", "1I04", "" ], [ "P02762-1", "protein_xref_pdb", "1I05", "" ], [ "P02762-1", "protein_xref_pdb", "1I06", "" ], [ "P02762-1", "protein_xref_pdb", "1MUP", "" ], [ "P02762-1", "protein_xref_pdb", "2LB6", "" ], [ "Q5EBH1-1", "protein_xref_pdb", "1RFH", "" ], [ "Q5EBH1-1", "protein_xref_pdb", "2FNF", "" ], [ "Q5EBH1-1", "protein_xref_pdb", "2YMY", "" ], [ "Q5EBH1-1", "protein_xref_pdb", "3DDC", "" ], [ "Q9EP73-1", "protein_xref_pdb", "6SRU", "" ], [ "O08912-1", "protein_xref_pdb", "1XHB", "" ], [ "Q66GT5-1", "protein_xref_pdb", "3RGO", "" ], [ "Q66GT5-1", "protein_xref_pdb", "3RGQ", "" ], [ "Q69Z98-1", "protein_xref_pdb", "4YNZ", "" ], [ "Q69Z98-1", "protein_xref_pdb", "4YOM", "" ], [ "Q5NCY0-1", "protein_xref_pdb", "4EZH", "" ], [ "Q5NCY0-1", "protein_xref_pdb", "4EYU", "" ], [ "Q5NCY0-1", "protein_xref_pdb", "4EZ4", "" ], [ "Q9ESN9-1", "protein_xref_pdb", "6EJN", "" ], [ "Q9ESN4-1", "protein_xref_pdb", "5YBZ", "" ], [ "Q9ESN4-1", "protein_xref_pdb", "4QQH", "" ], [ "Q9ESN4-1", "protein_xref_pdb", "4QQL", "" ], [ "Q9ESN4-1", "protein_xref_pdb", "4QQO", "" ], [ "Q9ESN4-1", "protein_xref_pdb", "4QQP", "" ], [ "Q149C2-1", "protein_xref_pdb", "5FMU", "" ], [ "O88447-1", "protein_xref_pdb", "6SWU", "" ], [ "Q8C0V1-1", "protein_xref_pdb", "1X58", "" ], [ "Q9R002-1", "protein_xref_pdb", "4JBJ", "" ], [ "Q9R002-1", "protein_xref_pdb", "4JBK", "" ], [ "Q9R002-1", "protein_xref_pdb", "4L5Q", "" ], [ "Q9R002-1", "protein_xref_pdb", "4L5R", "" ], [ "Q9R002-1", "protein_xref_pdb", "4L5S", "" ], [ "Q9R002-1", "protein_xref_pdb", "4L5T", "" ], [ "Q9R002-1", "protein_xref_pdb", "4LNQ", "" ], [ "O70133-1", "protein_xref_pdb", "1UIL", "" ], [ "O70133-1", "protein_xref_pdb", "1WHQ", "" ], [ "O70133-1", "protein_xref_pdb", "2RS6", "" ], [ "O70133-1", "protein_xref_pdb", "2RS7", "" ], [ "Q9CZB6-1", "protein_xref_pdb", "6W1S", "" ], [ "Q9QZQ0-1", "protein_xref_pdb", "5SY7", "" ], [ "P16297-1", "protein_xref_pdb", "6DG5", "" ], [ "P62281-1", "protein_xref_pdb", "7CPU", "" ], [ "P62281-1", "protein_xref_pdb", "7CPV", "" ], [ "P62281-1", "protein_xref_pdb", "7LS1", "" ], [ "P62281-1", "protein_xref_pdb", "7LS2", "" ], [ "P14429-1", "protein_xref_pdb", "1K8D", "" ], [ "Q9R0M5-1", "protein_xref_pdb", "1IG3", "" ], [ "Q9R0M5-1", "protein_xref_pdb", "2F17", "" ], [ "Q9R0M6-1", "protein_xref_pdb", "1YZL", "" ], [ "Q9R0M6-1", "protein_xref_pdb", "4QXA", "" ], [ "O88491-1", "protein_xref_pdb", "2NAA", "" ], [ "P57080-1", "protein_xref_pdb", "1VDL", "" ], [ "O09130-1", "protein_xref_pdb", "3A4R", "" ], [ "O09130-1", "protein_xref_pdb", "3A4S", "" ], [ "Q8CG03-1", "protein_xref_pdb", "2K31", "" ], [ "P42228-1", "protein_xref_pdb", "1BGF", "" ], [ "Q9EPK5-1", "protein_xref_pdb", "5GN0", "" ], [ "Q02395-1", "protein_xref_pdb", "2EQJ", "" ], [ "Q02395-1", "protein_xref_pdb", "2YT5", "" ], [ "P01863-1", "protein_xref_pdb", "1PG7", "" ], [ "P01863-1", "protein_xref_pdb", "2IPU", "" ], [ "P01863-1", "protein_xref_pdb", "2R0W", "" ], [ "P01863-1", "protein_xref_pdb", "1FE8", "" ], [ "P01863-1", "protein_xref_pdb", "4KVC", "" ], [ "P01863-1", "protein_xref_pdb", "2ZCH", "" ], [ "P01863-1", "protein_xref_pdb", "2ZCK", "" ] ] }, "readme": "Name\n - Mouse UniProtKB Xref PDB\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2019-03-15T15:11:39.076274\n\nModified on\n - 2022-09-26T08:56:48.465547\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 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/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-mus-musculus.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-mus-musculus.nt\n Output Subdomain\n Name: mouse_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_xref_pdb.csv\n Name: mouse_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/mouse_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"2271\"\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: \"6496\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.1.1/reviewed/mouse_protein_xref_pdb.csv" }