{ "bcoid": "GLY_000669", "title": "Fruitfly UniProtKB Xref PDB", "description": "The Fruitfly UniProtKB Xref PDB contains fruitfly [taxid:7227] UniProtKB canonical accessions cross-referenced ...", "filename": "fruitfly_protein_xref_pdb.csv", "filetype": "csv", "categories": { "species": [ "Drosophila melanogaster" ], "molecule": [ "Protein" ], "tags": [ "Pdb cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P40427-1...", "protein_xref..." ], [ "P40427-1...", "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" } ], [ "P40427-1", "protein_xref_pdb", "1B8I", "" ], [ "P40427-1", "protein_xref_pdb", "2R5Y", "" ], [ "P40427-1", "protein_xref_pdb", "2R5Z", "" ], [ "P40427-1", "protein_xref_pdb", "5ZJQ", "" ], [ "P40427-1", "protein_xref_pdb", "5ZJR", "" ], [ "P40427-1", "protein_xref_pdb", "5ZJS", "" ], [ "P40427-1", "protein_xref_pdb", "5ZJT", "" ], [ "P40427-1", "protein_xref_pdb", "4CYC", "" ], [ "P40427-1", "protein_xref_pdb", "4UUS", "" ], [ "Q9VLI9-1", "protein_xref_pdb", "7B6D", "" ], [ "Q9VLI9-1", "protein_xref_pdb", "7B6R", "" ], [ "Q9VLI9-1", "protein_xref_pdb", "7B70", "" ], [ "Q9VLI9-1", "protein_xref_pdb", "7B6X", "" ], [ "M9PB30-1", "protein_xref_pdb", "1OIG", "" ], [ "P48555-1", "protein_xref_pdb", "5CM8", "" ], [ "P48555-1", "protein_xref_pdb", "5CM9", "" ], [ "A0A0B4JDC9-1", "protein_xref_pdb", "4Z88", "" ], [ "A0A0B4JDC9-1", "protein_xref_pdb", "4Z89", "" ], [ "A0A0B4JDC9-1", "protein_xref_pdb", "4Z8A", "" ], [ "A0A0B4JDC9-1", "protein_xref_pdb", "6Q9M", "" ], [ "P06602-1", "protein_xref_pdb", "1JGG", "" ], [ "P06603-1", "protein_xref_pdb", "6TIS", "" ], [ "P06603-1", "protein_xref_pdb", "6TIU", "" ], [ "P06603-1", "protein_xref_pdb", "6TIY", "" ], [ "P06603-1", "protein_xref_pdb", "6TIZ", "" ], [ "P06603-1", "protein_xref_pdb", "7QUC", "" ], [ "P06603-1", "protein_xref_pdb", "7QUD", "" ], [ "P06603-1", "protein_xref_pdb", "7QUP", "" ], [ "P06601-1", "protein_xref_pdb", "1FJL", "" ], [ "P06601-1", "protein_xref_pdb", "1PDN", "" ], [ "P25823-1", "protein_xref_pdb", "3NTH", "" ], [ "P25823-1", "protein_xref_pdb", "3NTI", "" ], [ "P25823-1", "protein_xref_pdb", "3NTK", "" ], [ "P25823-1", "protein_xref_pdb", "4Q5W", "" ], [ "P25823-1", "protein_xref_pdb", "4Q5Y", "" ], [ "P25822-1", "protein_xref_pdb", "3H3D", "" ], [ "P25822-1", "protein_xref_pdb", "5KLA", "" ], [ "P25822-1", "protein_xref_pdb", "5KL1", "" ], [ "P25822-1", "protein_xref_pdb", "5KL8", "" ], [ "P41092-1", "protein_xref_pdb", "4V6W", "" ], [ "P41092-1", "protein_xref_pdb", "6XU6", "" ], [ "P41092-1", "protein_xref_pdb", "6XU7", "" ], [ "P41092-1", "protein_xref_pdb", "6XU8", "" ], [ "P41093-1", "protein_xref_pdb", "4V6W", "" ], [ "P41093-1", "protein_xref_pdb", "6XU6", "" ], [ "P41093-1", "protein_xref_pdb", "6XU7", "" ], [ "P41093-1", "protein_xref_pdb", "6XU8", "" ], [ "P41094-1", "protein_xref_pdb", "4V6W", "" ], [ "P41094-1", "protein_xref_pdb", "6XU6", "" ], [ "P41094-1", "protein_xref_pdb", "6XU7", "" ], [ "P41094-1", "protein_xref_pdb", "6XU8", "" ], [ "Q9VTP4-1", "protein_xref_pdb", "4V6W", "" ], [ "Q9VTP4-1", "protein_xref_pdb", "6XU6", "" ], [ "Q9VTP4-1", "protein_xref_pdb", "6XU7", "" ], [ "Q9VTP4-1", "protein_xref_pdb", "6XU8", "" ], [ "Q24117-1", "protein_xref_pdb", "3DVP", "" ], [ "Q24117-1", "protein_xref_pdb", "5E0L", "" ], [ "Q24117-1", "protein_xref_pdb", "5E0M", "" ], [ "Q24117-1", "protein_xref_pdb", "2PG1", "" ], [ "Q24117-1", "protein_xref_pdb", "2P2T", "" ], [ "Q24117-1", "protein_xref_pdb", "3FM7", "" ], [ "Q24117-1", "protein_xref_pdb", "1RHW", "" ], [ "Q24117-1", "protein_xref_pdb", "3BRI", "" ], [ "Q24117-1", "protein_xref_pdb", "3BRL", "" ], [ "Q24117-1", "protein_xref_pdb", "3DVH", "" ], [ "Q24117-1", "protein_xref_pdb", "3DVT", "" ], [ "Q24117-1", "protein_xref_pdb", "3E2B", "" ], [ "Q24117-1", "protein_xref_pdb", "3GLW", "" ], [ "Q24117-1", "protein_xref_pdb", "4QH7", "" ], [ "Q24117-1", "protein_xref_pdb", "4QH8", "" ], [ "Q24117-1", "protein_xref_pdb", "7K3J", "" ], [ "Q24117-1", "protein_xref_pdb", "7K3K", "" ], [ "Q24117-1", "protein_xref_pdb", "7K3L", "" ], [ "Q9VAK8-1", "protein_xref_pdb", "3ZZO", "" ], [ "Q9VAK8-1", "protein_xref_pdb", "3ZZR", "" ], [ "Q9W4R3-1", "protein_xref_pdb", "5EO9", "" ], [ "Q9W4R3-1", "protein_xref_pdb", "6EFY", "" ], [ "Q9W4R3-1", "protein_xref_pdb", "6NRQ", "" ], [ "Q9V3V9-1", "protein_xref_pdb", "3ISM", "" ], [ "Q9W4I7-1", "protein_xref_pdb", "5YI7", "" ], [ "Q9W4I7-1", "protein_xref_pdb", "5YI8", "" ], [ "Q9W237-1", "protein_xref_pdb", "4V6W", "" ], [ "Q9W237-1", "protein_xref_pdb", "6XU6", "" ], [ "Q9W237-1", "protein_xref_pdb", "6XU7", "" ] ] }, "readme": "Name\n - Fruitfly UniProtKB Xref PDB\n\nVersion\n - v-2.1.1\n\nCreated on\n - 2022-08-31T13:40:29.038163\n\nModified on\n - 2022-09-26T09:08:12.651444\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 Fruitfly UniProtKB Xref PDB contains fruitfly [taxid:7227] UniProtKB canonical accessions cross-referenced to PDB database accessions/identifiers. 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-drosophila-melanogaster.nt\n URI: /data/shared/glyds/downloads/ebi/2023_02/uniprot-proteome-drosophila-melanogaster.nt\n Output Subdomain\n Name: fruitfly_protein_xref_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/fruitfly_protein_xref_pdb.csv\n Name: fruitfly_protein_xref_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.1.1/reviewed/fruitfly_protein_xref_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"566\"\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: \"1158\"\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/fruitfly_protein_xref_pdb.csv" }