{ "bcoid": "GLY_000238", "title": "Rat UniProtKB Xref NCBI Gene", "description": "The Rat UniProtKB Xref NCBI Gene dataset contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced ...", "filename": "rat_protein_xref_geneid.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Ncbi Gene 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_geneid", "365192", "" ], [ "D3ZB49-1", "protein_xref_geneid", "313085", "" ], [ "D3ZB48-1", "protein_xref_geneid", "313370", "" ], [ "Q5RJZ1-1", "protein_xref_geneid", "362288", "" ], [ "Q0HA29-1", "protein_xref_geneid", "289095", "" ], [ "A0A0G2JVG8-1", "protein_xref_geneid", "405322", "" ], [ "Q99372-1", "protein_xref_geneid", "25043", "" ], [ "A0A096MJY4-1", "protein_xref_geneid", "499497", "" ], [ "A0A096MJY1-1", "protein_xref_geneid", "691984", "" ], [ "A0A0G2KA92-1", "protein_xref_geneid", "308738", "" ], [ "A0A0G2K4P4-1", "protein_xref_geneid", "500693", "" ], [ "Q5RJK6-1", "protein_xref_geneid", "316376", "" ], [ "Q62949-1", "protein_xref_geneid", "25305", "" ], [ "P01946-1", "protein_xref_geneid", "25632", "" ], [ "P01946-1", "protein_xref_geneid", "360504", "" ], [ "Q5M9G9-1", "protein_xref_geneid", "360977", "" ], [ "O35152-1", "protein_xref_geneid", "54400", "" ], [ "P30936-1", "protein_xref_geneid", "171044", "" ], [ "O35158-1", "protein_xref_geneid", "50938", "" ], [ "P02761-1", "protein_xref_geneid", "259246", "" ], [ "P02764-1", "protein_xref_geneid", "24614", "" ], [ "P02767-1", "protein_xref_geneid", "24856", "" ], [ "D4A4W8-1", "protein_xref_geneid", "292301", "" ], [ "D4A4W0-1", "protein_xref_geneid", "293781", "" ], [ "D4A4W1-1", "protein_xref_geneid", "681398", "" ], [ "F7EN52-1", "protein_xref_geneid", "362782", "" ], [ "D4A4W4-1", "protein_xref_geneid", "366836", "" ], [ "D4A4W5-1", "protein_xref_geneid", "303056", "" ], [ "D4A4W6-1", "protein_xref_geneid", "688717", "" ], [ "D4A4W7-1", "protein_xref_geneid", "689931", "" ], [ "G3V6I3-1", "protein_xref_geneid", "360613", "" ], [ "P21932-1", "protein_xref_geneid", "64508", "" ], [ "Q8K4K5-1", "protein_xref_geneid", "54265", "" ], [ "G3V6I6-1", "protein_xref_geneid", "289036", "" ], [ "G3V6I4-1", "protein_xref_geneid", "690745", "" ], [ "P12749-1", "protein_xref_geneid", "287417", "" ], [ "O08812-1", "protein_xref_geneid", "29485", "" ], [ "P39020-1", "protein_xref_geneid", "29279", "" ], [ "A0A0G2K0T8-1", "protein_xref_geneid", "684972", "" ], [ "Q6P6Q9-1", "protein_xref_geneid", "365567", "" ], [ "P28648-1", "protein_xref_geneid", "29186", "" ], [ "D3ZVR6-1", "protein_xref_geneid", "294601", "" ], [ "P01237-1", "protein_xref_geneid", "24683", "" ], [ "P01230-1", "protein_xref_geneid", "25329", "" ], [ "M0RB72-1", "protein_xref_geneid", "688163", "" ], [ "P09006-1", "protein_xref_geneid", "24795", "" ], [ "M0RB75-1", "protein_xref_geneid", "301128", "" ], [ "Q9JHY1-1", "protein_xref_geneid", "116479", "" ], [ "Q9JHY2-1", "protein_xref_geneid", "65042", "" ], [ "Q9JHY7-1", "protein_xref_geneid", "64041", "" ], [ "E9PU34-1", "protein_xref_geneid", "292268", "" ], [ "Q02874-1", "protein_xref_geneid", "29384", "" ], [ "P08699-1", "protein_xref_geneid", "83781", "" ], [ "P56558-1", "protein_xref_geneid", "26295", "" ], [ "P08011-1", "protein_xref_geneid", "171341", "" ], [ "Q8CJ58-1", "protein_xref_geneid", "261738", "" ], [ "P54690-1", "protein_xref_geneid", "29592", "" ], [ "Q99JD4-1", "protein_xref_geneid", "114514", "" ], [ "Q99JD1-1", "protein_xref_geneid", "171412", "" ], [ "Q99JD3-1", "protein_xref_geneid", "171151", "" ], [ "Q99JD2-1", "protein_xref_geneid", "85270", "" ], [ "P83748-1", "protein_xref_geneid", "287106", "" ], [ "P18508-1", "protein_xref_geneid", "29709", "" ], [ "P22002-1", "protein_xref_geneid", "24239", "" ], [ "M0R8G5-1", "protein_xref_geneid", "100363266", "" ], [ "Q02293-1", "protein_xref_geneid", "64511", "" ], [ "M0R8G9-1", "protein_xref_geneid", "300599", "" ], [ "D3ZGR8-1", "protein_xref_geneid", "405051", "" ], [ "D3ZGR6-1", "protein_xref_geneid", "499442", "" ], [ "D3ZGR7-1", "protein_xref_geneid", "288920", "" ], [ "Q8K5E0-1", "protein_xref_geneid", "66025", "" ], [ "Q9R1N3-1", "protein_xref_geneid", "117955", "" ], [ "D3ZIY3-1", "protein_xref_geneid", "361920", "" ], [ "P48550-1", "protein_xref_geneid", "25743", "" ], [ "D3ZFP5-1", "protein_xref_geneid", "691352", "" ], [ "D3ZFP4-1", "protein_xref_geneid", "316273", "" ], [ "D3ZFP7-1", "protein_xref_geneid", "293166", "" ], [ "D3ZFP6-1", "protein_xref_geneid", "308768", "" ], [ "D3ZYL2-1", "protein_xref_geneid", "292199", "" ], [ "D3ZYL3-1", "protein_xref_geneid", "685641", "" ], [ "D3ZYL0-1", "protein_xref_geneid", "306886", "" ], [ "D4A131-1", "protein_xref_geneid", "363023", "" ], [ "D4A130-1", "protein_xref_geneid", "405066", "" ], [ "D4A133-1", "protein_xref_geneid", "685232", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref NCBI Gene\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.965792\n\nModified on\n - 2022-01-19T12:41:01.385924\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 NCBI Gene dataset contains rat [taxid:10116] UniProtKB canonical accessions cross-referenced to NCBI Gene database accessions/identifiers. The dataset is derived from 2019-05 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. \n\nDescription Domain\n Keywords\n - gene id\n - NCBI gene\n - cross-reference\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are cross-referenced to NCBI Gene 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-rattus-norvegicus.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2021_04/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/rat_protein_xref_geneid.csv\n Name: rat_protein_xref_geneid.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/rat_protein_xref_geneid.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16619\"\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: \"16824\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.12.3/reviewed/rat_protein_xref_geneid.csv" }