{ "bcoid": "GLY_000257", "title": "Rat UniProtKB Xref OrthoDB", "description": "The Rat UniProtKB Xref OrthoDB contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_orthodb.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Orthodb cross-references", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "D3ZB44-1...", "protein_xref..." ], [ "D3ZB49-1...", "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" } ], [ "D3ZB44-1", "protein_xref_orthodb", "1318335at2759", "" ], [ "D3ZB49-1", "protein_xref_orthodb", "890629at2759", "" ], [ "D3ZB48-1", "protein_xref_orthodb", "398210at2759", "" ], [ "Q0HA29-1", "protein_xref_orthodb", "1308027at2759", "" ], [ "A0A0G2JVG8-1", "protein_xref_orthodb", "1126809at2759", "" ], [ "A0A096MJY4-1", "protein_xref_orthodb", "729387at2759", "" ], [ "A0A096MJY1-1", "protein_xref_orthodb", "611422at2759", "" ], [ "A0A0G2K4P4-1", "protein_xref_orthodb", "792496at2759", "" ], [ "Q5RJK6-1", "protein_xref_orthodb", "1096950at2759", "" ], [ "Q62949-1", "protein_xref_orthodb", "1614009at2759", "" ], [ "P01946-1", "protein_xref_orthodb", "1398217at2759", "" ], [ "Q5M9G9-1", "protein_xref_orthodb", "1209476at2759", "" ], [ "O35152-1", "protein_xref_orthodb", "1536545at2759", "" ], [ "P30936-1", "protein_xref_orthodb", "1011272at2759", "" ], [ "P02764-1", "protein_xref_orthodb", "1257041at2759", "" ], [ "P02767-1", "protein_xref_orthodb", "1453185at2759", "" ], [ "D4A4W8-1", "protein_xref_orthodb", "1201455at2759", "" ], [ "D4A4W0-1", "protein_xref_orthodb", "979582at2759", "" ], [ "D4A4W1-1", "protein_xref_orthodb", "1612806at2759", "" ], [ "F7EN52-1", "protein_xref_orthodb", "825914at2759", "" ], [ "D4A4W4-1", "protein_xref_orthodb", "616687at2759", "" ], [ "D4A4W5-1", "protein_xref_orthodb", "587717at2759", "" ], [ "D4A4W6-1", "protein_xref_orthodb", "1587548at2759", "" ], [ "D4A4W7-1", "protein_xref_orthodb", "1441982at2759", "" ], [ "G3V6I3-1", "protein_xref_orthodb", "1635950at2759", "" ], [ "P21932-1", "protein_xref_orthodb", "154265at2759", "" ], [ "Q8K4K5-1", "protein_xref_orthodb", "122541at2759", "" ], [ "G3V6I4-1", "protein_xref_orthodb", "919343at2759", "" ], [ "P12749-1", "protein_xref_orthodb", "1488916at2759", "" ], [ "O08812-1", "protein_xref_orthodb", "439017at2759", "" ], [ "P39020-1", "protein_xref_orthodb", "1522857at2759", "" ], [ "Q6P6Q9-1", "protein_xref_orthodb", "707988at2759", "" ], [ "P28648-1", "protein_xref_orthodb", "1467737at2759", "" ], [ "D3ZVR6-1", "protein_xref_orthodb", "1003628at2759", "" ], [ "P01237-1", "protein_xref_orthodb", "1290070at2759", "" ], [ "P01230-1", "protein_xref_orthodb", "1060061at2759", "" ], [ "M0RB72-1", "protein_xref_orthodb", "1542535at2759", "" ], [ "P09006-1", "protein_xref_orthodb", "1124079at2759", "" ], [ "M0RB75-1", "protein_xref_orthodb", "1186832at2759", "" ], [ "Q9JHY1-1", "protein_xref_orthodb", "1122085at2759", "" ], [ "Q9JHY2-1", "protein_xref_orthodb", "881974at2759", "" ], [ "Q9JHY7-1", "protein_xref_orthodb", "1404665at2759", "" ], [ "E9PU34-1", "protein_xref_orthodb", "954411at2759", "" ], [ "Q02874-1", "protein_xref_orthodb", "1504122at2759", "" ], [ "P08699-1", "protein_xref_orthodb", "829777at2759", "" ], [ "P08011-1", "protein_xref_orthodb", "1591261at2759", "" ], [ "Q8CJ58-1", "protein_xref_orthodb", "1188976at2759", "" ], [ "P54690-1", "protein_xref_orthodb", "853728at2759", "" ], [ "Q99JD4-1", "protein_xref_orthodb", "66632at2759", "" ], [ "Q99JD1-1", "protein_xref_orthodb", "1608276at2759", "" ], [ "Q99JD3-1", "protein_xref_orthodb", "1236425at2759", "" ], [ "Q99JD2-1", "protein_xref_orthodb", "581072at2759", "" ], [ "P18508-1", "protein_xref_orthodb", "1057372at2759", "" ], [ "P22002-1", "protein_xref_orthodb", "172471at2759", "" ], [ "M0R8G5-1", "protein_xref_orthodb", "1624806at2759", "" ], [ "Q02293-1", "protein_xref_orthodb", "1042804at2759", "" ], [ "M0R8G9-1", "protein_xref_orthodb", "1075792at2759", "" ], [ "D3ZGR8-1", "protein_xref_orthodb", "987071at2759", "" ], [ "D3ZGR6-1", "protein_xref_orthodb", "852769at2759", "" ], [ "D3ZGR7-1", "protein_xref_orthodb", "1538520at2759", "" ], [ "D3ZGR5-1", "protein_xref_orthodb", "854133at2759", "" ], [ "Q8K5E0-1", "protein_xref_orthodb", "854783at2759", "" ], [ "Q9R1N3-1", "protein_xref_orthodb", "265068at2759", "" ], [ "D3ZIY3-1", "protein_xref_orthodb", "1523251at2759", "" ], [ "P48550-1", "protein_xref_orthodb", "956263at2759", "" ], [ "D3ZFP5-1", "protein_xref_orthodb", "1485195at2759", "" ], [ "D3ZFP4-1", "protein_xref_orthodb", "266497at2759", "" ], [ "D3ZFP7-1", "protein_xref_orthodb", "569133at2759", "" ], [ "D3ZFP6-1", "protein_xref_orthodb", "150355at2759", "" ], [ "D3ZYL2-1", "protein_xref_orthodb", "215408at2759", "" ], [ "D3ZYL3-1", "protein_xref_orthodb", "546292at2759", "" ], [ "D3ZYL0-1", "protein_xref_orthodb", "346354at2759", "" ], [ "D4A131-1", "protein_xref_orthodb", "1592747at2759", "" ], [ "D4A133-1", "protein_xref_orthodb", "241249at2759", "" ], [ "P09875-1", "protein_xref_orthodb", "508327at2759", "" ], [ "D4A138-1", "protein_xref_orthodb", "1198436at2759", "" ], [ "D3ZCS5-1", "protein_xref_orthodb", "1595761at2759", "" ], [ "D3ZCS4-1", "protein_xref_orthodb", "674320at2759", "" ], [ "D3ZHE2-1", "protein_xref_orthodb", "1457080at2759", "" ], [ "D3ZHE3-1", "protein_xref_orthodb", "287340at2759", "" ], [ "D3ZCS1-1", "protein_xref_orthodb", "1416350at2759", "" ], [ "D3ZHE5-1", "protein_xref_orthodb", "1419449at2759", "" ], [ "D3ZCS2-1", "protein_xref_orthodb", "1258047at2759", "" ], [ "Q9JIL8-1", "protein_xref_orthodb", "179362at2759", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref OrthoDB\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.984081\n\nModified on\n - 2022-01-19T13:32:51.015878\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 Rat UniProtKB Xref OrthoDB contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to OrthoDB 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 - OrthoDB is a comprehensive catalog of orthologs, i.e. descendants from a single gene of the last common ancestor of a specific phylogeny radiation termed level-of-orthology. \n\nDescription Domain\n Keywords\n - orthologs\n - OrthoDB\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to OrthoDB 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: rat_protein_masterlist.csv\n URI: https://data.glygen.org//ln2data/releases/data/v-1.11.2/reviewed/rat_protein_masterlist.csv\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org//ln2downloads/ebi/2021_03/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_orthodb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_orthodb.csv\n Name: rat_protein_xref_orthodb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_orthodb.stat.csv", "downloadurl": "/ln2data/releases/data/v-1.12.1/reviewed/rat_protein_xref_orthodb.csv" }