{ "bcoid": "GLY_000790", "title": "Yeast UniProtKB Xref OrthoDB", "description": "The Yeast UniProtKB Xref OrthoDB contains yeast [taxid:559292] UniProtKB canonical accessions cross-referenced ...", "filename": "yeast_protein_xref_orthodb.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Orthodb cross-references" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "protein_xref..." ], [ "P39970-1...", "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" } ], [ "P30619-1", "protein_xref_orthodb", "4609640at2759", "" ], [ "P39970-1", "protein_xref_orthodb", "1409438at2759", "" ], [ "P39971-1", "protein_xref_orthodb", "2039696at2759", "" ], [ "P39976-1", "protein_xref_orthodb", "1664005at2759", "" ], [ "P39977-1", "protein_xref_orthodb", "5539949at2759", "" ], [ "P39974-1", "protein_xref_orthodb", "2024691at2759", "" ], [ "P39975-1", "protein_xref_orthodb", "1968086at2759", "" ], [ "P39979-1", "protein_xref_orthodb", "5232122at2759", "" ], [ "Q07959-1", "protein_xref_orthodb", "373478at2759", "" ], [ "P0CX69-1", "protein_xref_orthodb", "2039326at2759", "" ], [ "P25379-1", "protein_xref_orthodb", "8406at2759", "" ], [ "P25378-1", "protein_xref_orthodb", "8685at2759", "" ], [ "P17121-1", "protein_xref_orthodb", "25175at2759", "" ], [ "P25374-1", "protein_xref_orthodb", "212394at2759", "" ], [ "P17123-1", "protein_xref_orthodb", "2035813at2759", "" ], [ "P17122-1", "protein_xref_orthodb", "2018902at2759", "" ], [ "P25371-1", "protein_xref_orthodb", "359054at2759", "" ], [ "P25370-1", "protein_xref_orthodb", "1709736at2759", "" ], [ "P25373-1", "protein_xref_orthodb", "203654at2759", "" ], [ "P25372-1", "protein_xref_orthodb", "45858at2759", "" ], [ "Q06568-1", "protein_xref_orthodb", "2014254at2759", "" ], [ "Q03049-1", "protein_xref_orthodb", "1200131at2759", "" ], [ "Q06567-1", "protein_xref_orthodb", "177137at2759", "" ], [ "Q06563-1", "protein_xref_orthodb", "314578at2759", "" ], [ "Q00539-1", "protein_xref_orthodb", "129910at2759", "" ], [ "Q07748-1", "protein_xref_orthodb", "45357at2759", "" ], [ "Q07963-1", "protein_xref_orthodb", "51389at2759", "" ], [ "Q00246-1", "protein_xref_orthodb", "2016743at2759", "" ], [ "Q00245-1", "protein_xref_orthodb", "5480056at2759", "" ], [ "P0CX61-1", "protein_xref_orthodb", "2039326at2759", "" ], [ "P40422-1", "protein_xref_orthodb", "5489148at2759", "" ], [ "P0CX62-1", "protein_xref_orthodb", "2039326at2759", "" ], [ "P0CX64-1", "protein_xref_orthodb", "2039326at2759", "" ], [ "P0CX67-1", "protein_xref_orthodb", "2039326at2759", "" ], [ "P18494-1", "protein_xref_orthodb", "318925at2759", "" ], [ "P18496-1", "protein_xref_orthodb", "2912201at2759", "" ], [ "Q03441-1", "protein_xref_orthodb", "10607at2759", "" ], [ "Q08748-1", "protein_xref_orthodb", "1984726at2759", "" ], [ "Q08749-1", "protein_xref_orthodb", "2782446at2759", "" ], [ "Q08746-1", "protein_xref_orthodb", "5478574at2759", "" ], [ "Q08747-1", "protein_xref_orthodb", "5490826at2759", "" ], [ "Q08745-1", "protein_xref_orthodb", "154729at2759", "" ], [ "Q08742-1", "protein_xref_orthodb", "35609at2759", "" ], [ "Q08743-1", "protein_xref_orthodb", "1438495at2759", "" ], [ "P32915-1", "protein_xref_orthodb", "166798at2759", "" ], [ "P32914-1", "protein_xref_orthodb", "130469at2759", "" ], [ "P32917-1", "protein_xref_orthodb", "2733863at2759", "" ], [ "P32916-1", "protein_xref_orthodb", "5475029at2759", "" ], [ "P32911-1", "protein_xref_orthodb", "1329568at2759", "" ], [ "P32910-1", "protein_xref_orthodb", "930780at2759", "" ], [ "P32913-1", "protein_xref_orthodb", "1708746at2759", "" ], [ "P32912-1", "protein_xref_orthodb", "2019972at2759", "" ], [ "Q04438-1", "protein_xref_orthodb", "2018217at2759", "" ], [ "Q04439-1", "protein_xref_orthodb", "1094820at2759", "" ], [ "Q04430-1", "protein_xref_orthodb", "167164at2759", "" ], [ "Q04431-1", "protein_xref_orthodb", "2035137at2759", "" ], [ "Q04432-1", "protein_xref_orthodb", "4342at2759", "" ], [ "Q04433-1", "protein_xref_orthodb", "2039783at2759", "" ], [ "Q04437-1", "protein_xref_orthodb", "2056550at2759", "" ], [ "P00546-1", "protein_xref_orthodb", "244018at2759", "" ], [ "P04385-1", "protein_xref_orthodb", "177392at2759", "" ], [ "P04387-1", "protein_xref_orthodb", "2735190at2759", "" ], [ "P04386-1", "protein_xref_orthodb", "5478070at2759", "" ], [ "Q08299-1", "protein_xref_orthodb", "2165012at2759", "" ], [ "Q08562-1", "protein_xref_orthodb", "200191at2759", "" ], [ "Q08560-1", "protein_xref_orthodb", "2019308at2759", "" ], [ "Q08561-1", "protein_xref_orthodb", "2039480at2759", "" ], [ "P25377-1", "protein_xref_orthodb", "5353053at2759", "" ], [ "P25376-1", "protein_xref_orthodb", "2024136at2759", "" ], [ "P32474-1", "protein_xref_orthodb", "2021174at2759", "" ], [ "P09007-1", "protein_xref_orthodb", "728091at2759", "" ], [ "P04037-1", "protein_xref_orthodb", "1320at2759", "" ], [ "P04039-1", "protein_xref_orthodb", "2036197at2759", "" ], [ "Q05955-1", "protein_xref_orthodb", "2035251at2759", "" ], [ "P00724-1", "protein_xref_orthodb", "1105221at2759", "" ], [ "P00729-1", "protein_xref_orthodb", "1647009at2759", "" ], [ "Q03048-1", "protein_xref_orthodb", "3380386at2759", "" ], [ "P50896-1", "protein_xref_orthodb", "162831at2759", "" ], [ "P32786-1", "protein_xref_orthodb", "1985712at2759", "" ], [ "Q02872-1", "protein_xref_orthodb", "2013630at2759", "" ], [ "Q02873-1", "protein_xref_orthodb", "1409201at2759", "" ], [ "Q02875-1", "protein_xref_orthodb", "5406906at2759", "" ], [ "P36096-1", "protein_xref_orthodb", "51730at2759", "" ], [ "Q10740-1", "protein_xref_orthodb", "443480at2759", "" ] ] }, "readme": "Name\n - Yeast UniProtKB Xref OrthoDB\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2022-08-31T13:25:53.921490\n\nModified on\n - 2023-09-11T20:28:54\n\nCreated by\n - [jeetvora@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Yeast UniProtKB Xref OrthoDB contains yeast [taxid:559292] UniProtKB canonical accessions cross-referenced to OrthoDB database accessions/identifiers. 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/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-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_13/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_xref_orthodb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_xref_orthodb.csv\n Name: yeast_protein_xref_orthodb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_xref_orthodb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5773\"\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: \"4376\"\n Name: \"xref_label\"\n Description: \"Label/Name associated with x-ref\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/yeast_protein_xref_orthodb.csv" }