{ "bcoid": "GLY_000751", "title": "Yeast Gene Locus (Ensembl)", "description": "The Yeast Gene Locus (Ensembl) contains yeast [taxid:559292] UniProtKB canonical accessions mapped to ...", "filename": "yeast_protein_genelocus.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Gene Coordinates" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "SEC1..." ], [ "P39970-1...", "ACA1..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "ensembl_gene_id" }, { "type": "string", "label": "chromosome_id" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "strand" } ], [ "P30619-1", "SEC1", "YDR164C", "IV", "782041", "784215", "0" ], [ "P39970-1", "ACA1", "YER045C", "V", "240032", "241501", "0" ], [ "P39976-1", "DLD3", "YEL071W", "V", "16355", "17845", "1" ], [ "P39975-1", "RMD6", "YEL072W", "V", "13720", "14415", "1" ], [ "P39979-1", "HPA3", "YEL066W", "V", "26667", "27206", "1" ], [ "P25379-1", "CHA1", "YCL064C", "III", "15798", "16880", "0" ], [ "P25378-1", "RHB1", "YCR027C", "III", "167370", "167999", "0" ], [ "P17121-1", "SAC7", "YDR389W", "IV", "1252537", "1254501", "1" ], [ "P25374-1", "NFS1", "YCL017C", "III", "92777", "94270", "0" ], [ "P17123-1", "SPO12", "YHR152W", "VIII", "401434", "401955", "1" ], [ "P17122-1", "SPO16", "YHR153C", "VIII", "402086", "402682", "0" ], [ "P25371-1", "ADP1", "YCR011C", "III", "133724", "136873", "0" ], [ "P25370-1", "GFD2", "YCL036W", "III", "59026", "60726", "1" ], [ "P25373-1", "GRX1", "YCL035C", "III", "60841", "61173", "0" ], [ "P25372-1", "TRX3", "YCR083W", "III", "259578", "259961", "1" ], [ "Q03048-1", "COF1", "YLL050C", "XII", "39804", "40414", "0" ], [ "Q06567-1", "MCP2", "YLR253W", "XII", "642627", "644336", "1" ], [ "Q06563-1", "SYM1", "YLR251W", "XII", "641464", "642057", "1" ], [ "Q00539-1", "NAM8", "YHR086W", "VIII", "278153", "279724", "1" ], [ "Q07748-1", "THI13", "YDL244W", "IV", "16204", "17226", "1" ], [ "Q07963-1", "UBR2", "YLR024C", "XII", "187663", "193281", "0" ], [ "Q00246-1", "RHO4", "YKR055W", "XI", "548216", "549091", "1" ], [ "Q00245-1", "RHO3", "YIL118W", "IX", "139752", "140447", "1" ], [ "P40422-1", "RPC10", "YHR143W-A", "VIII", "387233", "387445", "1" ], [ "P48566-1", "MSB3", "YNL293W", "XIV", "80640", "82541", "1" ], [ "P18494-1", "GLN3", "YER040W", "V", "229795", "231987", "1" ], [ "P18496-1", "ATP10", "YLR393W", "XII", "907079", "907918", "1" ], [ "Q08749-1", "TIM18", "YOR297C", "XV", "874743", "875321", "0" ], [ "Q08746-1", "RRS1", "YOR294W", "XV", "868340", "868951", "1" ], [ "Q08747-1", "UAF30", "YOR295W", "XV", "869208", "869894", "1" ], [ "Q08745-1", "RPS10A", "YOR293W", "XV", "867098", "867852", "1" ], [ "Q08742-1", "RDL2", "YOR286W", "XV", "850280", "850729", "1" ], [ "P32915-1", "SEC61", "YLR378C", "XII", "875736", "877178", "0" ], [ "P32914-1", "SPT4", "YGR063C", "VII", "617516", "617824", "0" ], [ "P32917-1", "STE5", "YDR103W", "IV", "658350", "661103", "1" ], [ "P32916-1", "SRP101", "YDR292C", "IV", "1043146", "1045011", "0" ], [ "P32911-1", "SUI1", "YNL244C", "XIV", "187170", "187496", "0" ], [ "P32910-1", "RPC34", "YNR003C", "XIV", "634344", "635297", "0" ], [ "P32913-1", "VPS17", "YOR132W", "XV", "573175", "574830", "1" ], [ "P32912-1", "VAM7", "YGL212W", "VII", "91432", "92382", "1" ], [ "Q04438-1", "SPG4", "YMR107W", "XIII", "483014", "483361", "1" ], [ "Q04439-1", "MYO5", "YMR109W", "XIII", "486587", "490246", "1" ], [ "Q04430-1", "CAB1", "YDR531W", "IV", "1498232", "1499335", "1" ], [ "Q04431-1", "KRE28", "YDR532C", "IV", "1499396", "1500553", "0" ], [ "Q04432-1", "HSP31", "YDR533C", "IV", "1501447", "1502160", "0" ], [ "Q04433-1", "FIT1", "YDR534C", "IV", "1503314", "1504900", "0" ], [ "Q04437-1", "YKU80", "YMR106C", "XIII", "478301", "480190", "0" ], [ "P00546-1", "CDC28", "YBR160W", "II", "560078", "560974", "1" ], [ "P04385-1", "GAL1", "YBR020W", "II", "279021", "280607", "1" ], [ "P04387-1", "GAL80", "YML051W", "XIII", "171594", "172901", "1" ], [ "P04386-1", "GAL4", "YPL248C", "XVI", "79711", "82356", "0" ], [ "Q08299-1", "ENB1", "YOL158C", "XV", "19491", "21311", "0" ], [ "Q08562-1", "ULS1", "YOR191W", "XV", "692475", "697334", "1" ], [ "Q08561-1", "IES4", "YOR189W", "XV", "689624", "689974", "1" ], [ "P25377-1", "ADH7", "YCR105W", "III", "309070", "310155", "1" ], [ "P25376-1", "AGP1", "YCL025C", "III", "76018", "77919", "0" ], [ "P09007-1", "SRD1", "YCR018C", "III", "148238", "148903", "0" ], [ "P04037-1", "COX4", "YGL187C", "VII", "149704", "150171", "0" ], [ "P04039-1", "COX8", "YLR395C", "XII", "909729", "909965", "0" ], [ "Q05779-1", "COQ9", "YLR201C", "XII", "549511", "550293", "0" ], [ "P00724-1", "SUC2", "YIL162W", "IX", "37385", "38983", "1" ], [ "P00729-1", "PRC1", "YMR297W", "XIII", "861922", "863520", "1" ], [ "Q06568-1", "NDL1", "YLR254C", "XII", "644404", "644973", "0" ], [ "Q04689-1", "AIM32", "YML050W", "XIII", "173139", "174074", "1" ], [ "P36094-1", "SPC42", "YKL042W", "XI", "358475", "359566", "1" ], [ "Q02875-1", "SYH1", "YPL105C", "XVI", "352863", "355412", "0" ], [ "P23542-1", "AAT2", "YLR027C", "XII", "196829", "198085", "0" ], [ "Q05473-1", "MRX8", "YDR336W", "IV", "1145092", "1146036", "1" ], [ "Q05471-1", "SWR1", "YDR334W", "IV", "1135932", "1140476", "1" ], [ "Q3E7A9-1", "CMC4", "YMR194C-B", "XIII", "652594", "652887", "0" ], [ "P53045-1", "ERG25", "YGR060W", "VII", "610564", "611493", "1" ], [ "P53043-1", "PPT1", "YGR123C", "VII", "736662", "738203", "0" ], [ "Q07747-1", "AAD4", "YDL243C", "IV", "17577", "18566", "0" ], [ "P19073-1", "CDC42", "YLR229C", "XII", "604212", "604787", "0" ], [ "Q04177-1", "UTP5", "YDR398W", "IV", "1267471", "1269402", "1" ], [ "P40165-1", "NNR1", "YNL200C", "XIV", "263713", "264453", "0" ], [ "P40164-1", "PSY2", "YNL201C", "XIV", "260627", "263203", "0" ], [ "P23748-1", "MIH1", "YMR036C", "XIII", "341856", "343520", "0" ], [ "P40161-1", "RTT106", "YNL206C", "XIV", "256788", "258155", "0" ], [ "P40160-1", "RIO2", "YNL207W", "XIV", "255353", "256630", "1" ], [ "P40309-1", "KHA1", "YJL094C", "X", "251821", "254442", "0" ], [ "P40308-1", "TGL3", "YMR313C", "XIII", "899379", "901307", "0" ], [ "P33734-1", "HIS7", "YBR248C", "II", "714807", "716465", "0" ], [ "P40302-1", "PRE5", "YMR314W", "XIII", "901709", "902413", "1" ] ] }, "readme": "Name\n - Yeast Gene Locus (Ensembl)\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2020-04-10T11:29:22.824792\n\nModified on\n - 2023-09-11T19:00:43\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], 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 Yeast Gene Locus (Ensembl) contains yeast [taxid:559292] UniProtKB canonical accessions mapped to the corresponding ensembl Gene ID, chromosome ID along with the gene's start and end position on the chromosome. The dataset is derived from 2019-09 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - gene coordinates\n - chromosome\n - start position\n - end position\n - Ensembl\n - strand\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB canonical accessions that are mapped to ENSEMBL Gene 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: yeast_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.csv\n Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_genelocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_genelocus.csv\n Name: yeast_protein_genelocus.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_genelocus.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5043\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"5043\"\n Name: \"ensembl_gene_id\"\n Description: \"Gene Identifier in Ensembl database\"\n Unique Values: \"5043\"\n Name: \"chromosome_id\"\n Description: \"Chromosome number identifier\"\n Unique Values: \"17\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"5023\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"5034\"\n Name: \"strand\"\n Description: \"The strand of the gene\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_genelocus.csv" }