{ "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": [ [ "Q5RJZ1-1...", "protein_xref..." ], [ "A0A0G2K1R8-1...", "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" } ], [ "Q5RJZ1-1", "protein_xref_geneid", "362288", "" ], [ "A0A0G2K1R8-1", "protein_xref_geneid", "300193", "" ], [ "Q0HA29-1", "protein_xref_geneid", "289095", "" ], [ "A0A0G2JVG5-1", "protein_xref_geneid", "102552378", "" ], [ "P30937-1", "protein_xref_geneid", "25555", "" ], [ "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", "" ], [ "D4A4W2-1", "protein_xref_geneid", "497921", "" ], [ "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", "" ], [ "Q4KLI2-1", "protein_xref_geneid", "295496", "" ], [ "P01237-1", "protein_xref_geneid", "24683", "" ], [ "P01230-1", "protein_xref_geneid", "25329", "" ], [ "P09006-1", "protein_xref_geneid", "24795", "" ], [ "Q9JHY1-1", "protein_xref_geneid", "116479", "" ], [ "Q9JHY2-1", "protein_xref_geneid", "65042", "" ], [ "Q9JHY7-1", "protein_xref_geneid", "64041", "" ], [ "Q9WU49-1", "protein_xref_geneid", "260416", "" ], [ "F1MAA4-1", "protein_xref_geneid", "362645", "" ], [ "P83748-1", "protein_xref_geneid", "287106", "" ], [ "P18508-1", "protein_xref_geneid", "29709", "" ], [ "P04757-1", "protein_xref_geneid", "25101", "" ], [ "A0A8I5Y6V4-1", "protein_xref_geneid", "498394", "" ], [ "A0A8I6A0U5-1", "protein_xref_geneid", "309650", "" ], [ "Q9Z0V5-1", "protein_xref_geneid", "85274", "" ], [ "Q9R1N3-1", "protein_xref_geneid", "117955", "" ], [ "D3ZIY3-1", "protein_xref_geneid", "361920", "" ], [ "Q62952-1", "protein_xref_geneid", "25418", "" ], [ "D3ZFP5-1", "protein_xref_geneid", "691352", "" ], [ "D3ZFP4-1", "protein_xref_geneid", "316273", "" ], [ "D3ZFP7-1", "protein_xref_geneid", "293166", "" ], [ "D3ZFP6-1", "protein_xref_geneid", "308768", "" ], [ "D3ZFP1-1", "protein_xref_geneid", "305812", "" ], [ "D4A131-1", "protein_xref_geneid", "363023", "" ], [ "D4A133-1", "protein_xref_geneid", "685232", "" ], [ "P09875-1", "protein_xref_geneid", "305264", "" ], [ "D4A138-1", "protein_xref_geneid", "288909", "" ], [ "A0A8I6ALX9-1", "protein_xref_geneid", "502711", "" ], [ "D3ZCS5-1", "protein_xref_geneid", "287634", "" ], [ "D3ZCS4-1", "protein_xref_geneid", "310621", "" ], [ "D3ZCS6-1", "protein_xref_geneid", "287820", "" ], [ "D3ZCS1-1", "protein_xref_geneid", "498246", "" ], [ "D3ZCS3-1", "protein_xref_geneid", "363133", "" ], [ "A0A3B0J1M6-1", "protein_xref_geneid", "497886", "" ], [ "D3ZCS9-1", "protein_xref_geneid", "293613", "" ], [ "A0A0G2KAH3-1", "protein_xref_geneid", "315497", "" ], [ "D3ZUF1-1", "protein_xref_geneid", "362133", "" ], [ "Q9JIL3-1", "protein_xref_geneid", "84472", "" ], [ "Q6P5P4-1", "protein_xref_geneid", "305970", "" ], [ "Q6P5P5-1", "protein_xref_geneid", "58827", "" ], [ "A0A0G2JVP1-1", "protein_xref_geneid", "360991", "" ], [ "Q6P5P3-1", "protein_xref_geneid", "309196", "" ], [ "D3ZXJ0-1", "protein_xref_geneid", "288626", "" ], [ "D3ZB41-1", "protein_xref_geneid", "103690110", "" ], [ "A0A8I5ZXW0-1", "protein_xref_geneid", "289280", "" ], [ "D3ZXJ5-1", "protein_xref_geneid", "308789", "" ], [ "P14669-1", "protein_xref_geneid", "25291", "" ], [ "A0A8I6ACH9-1", "protein_xref_geneid", "687127", "" ], [ "A0A0G2JVZ2-1", "protein_xref_geneid", "680117", "" ], [ "A0A0G2JVZ7-1", "protein_xref_geneid", "298543", "" ], [ "Q6AYA4-1", "protein_xref_geneid", "313878", "" ], [ "Q9QYH7-1", "protein_xref_geneid", "59301", "" ], [ "Q67ER9-1", "protein_xref_geneid", "680188", "" ], [ "D3ZT68-1", "protein_xref_geneid", "361060", "" ], [ "Q9EPW1-1", "protein_xref_geneid", "29657", "" ], [ "D3ZT66-1", "protein_xref_geneid", "287969", "" ], [ "D4AE80-1", "protein_xref_geneid", "361109", "" ], [ "D4AE81-1", "protein_xref_geneid", "679812", "" ], [ "D4AE82-1", "protein_xref_geneid", "361669", "" ], [ "D4AE85-1", "protein_xref_geneid", "503052", "" ], [ "A0A0G2K8J8-1", "protein_xref_geneid", "308218", "" ], [ "P43219-1", "protein_xref_geneid", "25024", "" ], [ "D3ZUP4-1", "protein_xref_geneid", "314325", "" ], [ "Q9ESR9-1", "protein_xref_geneid", "79248", "" ] ] }, "readme": "Name\n - Rat UniProtKB Xref NCBI Gene\n\nVersion\n - v-2.0.3\n\nCreated on\n - 2019-09-06T14:06:38.965792\n\nModified on\n - 2022-09-26T09:04:47.920655\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/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-rattus-norvegicus.nt\n URI: /data/shared/glyds/downloads/ebi/2022_05/uniprot-proteome-rattus-norvegicus.nt\n Output Subdomain\n Name: rat_protein_xref_geneid.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_xref_geneid.csv\n Name: rat_protein_xref_geneid.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.0.3/reviewed/rat_protein_xref_geneid.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"17046\"\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: \"17426\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.0.3/reviewed/rat_protein_xref_geneid.csv" }