{ "bcoid": "GLY_000776", "title": "Yeast Transcript Locus (Ensembl Transcript coordinates)", "description": "The Yeast Transcript Locus (Ensembl Transcript coordinates)s contains UniProtKB yeast [taxid:559292] ...", "filename": "yeast_protein_transcriptlocus.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "Transcript Coordinates" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P30619-1...", "P30619-1..." ], [ "P39972-1...", "P39972-1..." ] ], "headers": [ "uniprotkb_ca...", "uniprotkb_is..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "uniprotkb_isoform_ac" }, { "type": "string", "label": "transcript_id" }, { "type": "string", "label": "peptide_id" }, { "type": "string", "label": "chromosome_id" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "strand" } ], [ "P30619-1", "P30619-1", "YDR164C_mRNA", "YDR164C", "IV", "784215", "782044", "1" ], [ "P39972-1", "P39972-1", "YEL075C_mRNA", "YEL075C", "V", "5713", "5348", "1" ], [ "P39970-1", "P39970-1", "YER045C_mRNA", "YER045C", "V", "241501", "240035", "1" ], [ "P39971-1", "P39971-1", "YEL076C_mRNA", "YEL076C", "V", "5114", "4467", "1" ], [ "P39976-1", "P39976-1", "YEL071W_mRNA", "YEL071W", "V", "16355", "17842", "0" ], [ "P39977-1", "P39977-1", "YEL068C_mRNA", "YEL068C", "V", "25978", "25649", "1" ], [ "P39974-1", "P39974-1", "YEL073C_mRNA", "YEL073C", "V", "7553", "7233", "1" ], [ "P39975-1", "P39975-1", "YEL072W_mRNA", "YEL072W", "V", "13720", "14412", "0" ], [ "P39978-1", "P39978-1", "YEL067C_mRNA", "YEL067C", "V", "26776", "26192", "1" ], [ "P25379-1", "P25379-1", "YCL064C_mRNA", "YCL064C", "III", "16880", "15801", "1" ], [ "P25378-1", "P25378-1", "YCR027C_mRNA", "YCR027C", "III", "167999", "167373", "1" ], [ "P17121-1", "P17121-1", "YDR389W_mRNA", "YDR389W", "IV", "1252537", "1254498", "0" ], [ "P25374-1", "P25374-1", "YCL017C_mRNA", "YCL017C", "III", "94270", "92780", "1" ], [ "P17123-1", "P17123-1", "YHR152W_mRNA", "YHR152W", "VIII", "401434", "401952", "0" ], [ "P17122-1", "P17122-1", "YHR153C_mRNA", "YHR153C", "VIII", "402682", "402089", "1" ], [ "P25371-1", "P25371-1", "YCR011C_mRNA", "YCR011C", "III", "136873", "133727", "1" ], [ "P25370-1", "P25370-1", "YCL036W_mRNA", "YCL036W", "III", "59026", "60723", "0" ], [ "P25373-1", "P25373-1", "YCL035C_mRNA", "YCL035C", "III", "61173", "60844", "1" ], [ "P25372-1", "P25372-1", "YCR083W_mRNA", "YCR083W", "III", "259578", "259958", "0" ], [ "Q03048-1", "Q03048-1", "YLL050C_mRNA", "YLL050C", "XII", "40414", "39807", "1" ], [ "Q03049-1", "Q03049-1", "YDR541C_mRNA", "YDR541C", "IV", "1520698", "1519667", "1" ], [ "Q06567-1", "Q06567-1", "YLR253W_mRNA", "YLR253W", "XII", "642627", "644333", "0" ], [ "Q06563-1", "Q06563-1", "YLR251W_mRNA", "YLR251W", "XII", "641464", "642054", "0" ], [ "Q00539-1", "Q00539-1", "YHR086W_mRNA", "YHR086W", "VIII", "278153", "279721", "0" ], [ "Q07748-1", "Q07748-1", "YDL244W_mRNA", "YDL244W", "IV", "16204", "17223", "0" ], [ "Q07963-1", "Q07963-1", "YLR024C_mRNA", "YLR024C", "XII", "193281", "187666", "1" ], [ "Q07746-1", "Q07746-1", "YDL242W_mRNA", "YDL242W", "IV", "18959", "19309", "0" ], [ "Q07967-1", "Q07967-1", "YLR030W_mRNA", "YLR030W", "XII", "203290", "204078", "0" ], [ "Q00246-1", "Q00246-1", "YKR055W_mRNA", "YKR055W", "XI", "548216", "549088", "0" ], [ "Q00245-1", "Q00245-1", "YIL118W_mRNA", "YIL118W", "IX", "139752", "140444", "0" ], [ "P40422-1", "P40422-1", "YHR143W-A_mRNA", "YHR143W-A", "VIII", "387233", "387442", "0" ], [ "P48566-1", "P48566-1", "YNL293W_mRNA", "YNL293W", "XIV", "80640", "82538", "0" ], [ "P18494-1", "P18494-1", "YER040W_mRNA", "YER040W", "V", "229795", "231984", "0" ], [ "P18496-1", "P18496-1", "YLR393W_mRNA", "YLR393W", "XII", "907079", "907915", "0" ], [ "P48568-1", "P48568-1", "YDL186W_mRNA", "YDL186W", "IV", "125616", "126446", "0" ], [ "Q08748-1", "Q08748-1", "YOR296W_mRNA", "YOR296W", "XV", "870202", "874068", "0" ], [ "Q08749-1", "Q08749-1", "YOR297C_mRNA", "YOR297C", "XV", "875321", "874746", "1" ], [ "Q08746-1", "Q08746-1", "YOR294W_mRNA", "YOR294W", "XV", "868340", "868948", "0" ], [ "Q08747-1", "Q08747-1", "YOR295W_mRNA", "YOR295W", "XV", "869208", "869891", "0" ], [ "Q08745-1", "Q08745-1", "YOR293W_mRNA", "YOR293W", "XV", "867098", "867849", "0" ], [ "Q08742-1", "Q08742-1", "YOR286W_mRNA", "YOR286W", "XV", "850280", "850726", "0" ], [ "Q08743-1", "Q08743-1", "YOR292C_mRNA", "YOR292C", "XV", "866582", "865656", "1" ], [ "P32915-1", "P32915-1", "YLR378C_mRNA", "YLR378C", "XII", "877178", "875739", "1" ], [ "P32914-1", "P32914-1", "YGR063C_mRNA", "YGR063C", "VII", "617824", "617519", "1" ], [ "P32917-1", "P32917-1", "YDR103W_mRNA", "YDR103W", "IV", "658350", "661100", "0" ], [ "P32916-1", "P32916-1", "YDR292C_mRNA", "YDR292C", "IV", "1045011", "1043149", "1" ], [ "P32911-1", "P32911-1", "YNL244C_mRNA", "YNL244C", "XIV", "187496", "187173", "1" ], [ "P32910-1", "P32910-1", "YNR003C_mRNA", "YNR003C", "XIV", "635297", "634347", "1" ], [ "P32913-1", "P32913-1", "YOR132W_mRNA", "YOR132W", "XV", "573175", "574827", "0" ], [ "P32912-1", "P32912-1", "YGL212W_mRNA", "YGL212W", "VII", "91432", "92379", "0" ], [ "Q04438-1", "Q04438-1", "YMR107W_mRNA", "YMR107W", "XIII", "483014", "483358", "0" ], [ "Q04439-1", "Q04439-1", "YMR109W_mRNA", "YMR109W", "XIII", "486587", "490243", "0" ], [ "Q04430-1", "Q04430-1", "YDR531W_mRNA", "YDR531W", "IV", "1498232", "1499332", "0" ], [ "Q04431-1", "Q04431-1", "YDR532C_mRNA", "YDR532C", "IV", "1500553", "1499399", "1" ], [ "Q04432-1", "Q04432-1", "YDR533C_mRNA", "YDR533C", "IV", "1502160", "1501450", "1" ], [ "Q04433-1", "Q04433-1", "YDR534C_mRNA", "YDR534C", "IV", "1504900", "1503317", "1" ], [ "Q04436-1", "Q04436-1", "YMR103C_mRNA", "YMR103C", "XIII", "473264", "472905", "1" ], [ "Q04437-1", "Q04437-1", "YMR106C_mRNA", "YMR106C", "XIII", "480190", "478304", "1" ], [ "P00546-1", "P00546-1", "YBR160W_mRNA", "YBR160W", "II", "560078", "560971", "0" ], [ "P04385-1", "P04385-1", "YBR020W_mRNA", "YBR020W", "II", "279021", "280604", "0" ], [ "P04387-1", "P04387-1", "YML051W_mRNA", "YML051W", "XIII", "171594", "172898", "0" ], [ "P04386-1", "P04386-1", "YPL248C_mRNA", "YPL248C", "XVI", "82356", "79714", "1" ], [ "Q08299-1", "Q08299-1", "YOL158C_mRNA", "YOL158C", "XV", "21311", "19494", "1" ], [ "Q08562-1", "Q08562-1", "YOR191W_mRNA", "YOR191W", "XV", "692475", "697331", "0" ], [ "Q08560-1", "Q08560-1", "YOR186W_mRNA", "YOR186W", "XV", "683111", "683542", "0" ], [ "Q08561-1", "Q08561-1", "YOR189W_mRNA", "YOR189W", "XV", "689624", "689971", "0" ], [ "P25377-1", "P25377-1", "YCR105W_mRNA", "YCR105W", "III", "309070", "310152", "0" ], [ "P25376-1", "P25376-1", "YCL025C_mRNA", "YCL025C", "III", "77919", "76021", "1" ], [ "P09007-1", "P09007-1", "YCR018C_mRNA", "YCR018C", "III", "148903", "148241", "1" ], [ "P04037-1", "P04037-1", "YGL187C_mRNA", "YGL187C", "VII", "150171", "149707", "1" ], [ "P04039-1", "P04039-1", "YLR395C_mRNA", "YLR395C", "XII", "909965", "909732", "1" ], [ "Q05779-1", "Q05779-1", "YLR201C_mRNA", "YLR201C", "XII", "550293", "549514", "1" ], [ "P00724-1", "P00724-1", "YIL162W_mRNA", "YIL162W", "IX", "37385", "38980", "0" ], [ "P00729-1", "P00729-1", "YMR297W_mRNA", "YMR297W", "XIII", "861922", "863517", "0" ], [ "Q06568-1", "Q06568-1", "YLR254C_mRNA", "YLR254C", "XII", "644973", "644407", "1" ], [ "Q04689-1", "Q04689-1", "YML050W_mRNA", "YML050W", "XIII", "173139", "174071", "0" ], [ "Q02872-1", "Q02872-1", "YPL108W_mRNA", "YPL108W", "XVI", "348446", "348949", "0" ], [ "P36094-1", "P36094-1", "YKL042W_mRNA", "YKL042W", "XI", "358475", "359563", "0" ], [ "Q02875-1", "Q02875-1", "YPL105C_mRNA", "YPL105C", "XVI", "355412", "352866", "1" ], [ "P23542-1", "P23542-1", "YLR027C_mRNA", "YLR027C", "XII", "198085", "196832", "1" ], [ "Q05473-1", "Q05473-1", "YDR336W_mRNA", "YDR336W", "IV", "1145092", "1146033", "0" ], [ "Q05471-1", "Q05471-1", "YDR334W_mRNA", "YDR334W", "IV", "1135932", "1140473", "0" ], [ "Q04170-1", "Q04170-1", "YDR391C_mRNA", "YDR391C", "IV", "1258056", "1257361", "1" ], [ "Q3E7A9-1", "Q3E7A9-1", "YMR194C-B_mRNA", "YMR194C-B", "XIII", "652887", "652597", "1" ] ] }, "readme": "Name\n - Yeast Transcript Locus (Ensembl Transcript coordinates)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2022-08-31T11:17:02.109861\n\nModified on\n - 2023-09-11T20:17:54\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], 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 - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Yeast Transcript Locus (Ensembl Transcript coordinates)s contains UniProtKB yeast [taxid:559292] canonical accessions mapped to their isoforms with further mapping to the corresponding ENSEMBL Transcript ID, Peptide ID, chromosome ID along with the transcripts' start and end position. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n Keywords\n - transcript locus\n - ensembl transcript id\n - ensembl peptide id\n - chromosome\n - Ensembl\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB accessions that are mapped to UniProtKB isoforms and ENSEMBL Transcript and Peptide identifiers from the triplestore containing triples from nt file and maps it to the UniProtKB canonical accession to finally extract 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_transcriptlocus.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_transcriptlocus.csv\n Name: yeast_protein_transcriptlocus.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/yeast_protein_transcriptlocus.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5936\"\n Name: \"uniprotkb_isoform_ac\"\n Description: \"\"UniProtKB isoform that includes the canonical accession and other isoforms generated by alternative splicing\"\n Unique Values: \"5936\"\n Name: \"transcript_id\"\n Description: \"Transcript Identifier in Ensembl database\"\n Unique Values: \"5885\"\n Name: \"peptide_id\"\n Description: \"Protein identifier in Ensembl database\"\n Unique Values: \"5885\"\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: \"5865\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"5867\"\n Name: \"strand\"\n Description: \"The strand of the gene\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/yeast_protein_transcriptlocus.csv" }