{"id":"https://openalex.org/W2134193442","doi":"https://doi.org/10.1093/nar/gkj146","title":"EPD in its twentieth year: towards complete promoter coverage of selected model organisms","display_name":"EPD in its twentieth year: towards complete promoter coverage of selected model organisms","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2134193442","doi":"https://doi.org/10.1093/nar/gkj146","mag":"2134193442","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381980"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj146","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D82/3926336/gkj146.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D82/3926336/gkj146.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5105777249","display_name":"Christof Schmid","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"C. D. Schmid","raw_affiliation_strings":["Swiss Institute of Bioinformatics, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5105777249"],"corresponding_institution_ids":["https://openalex.org/I12708293"],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":{"value":3992,"currency":"USD","value_usd":3992},"fwci":17.593,"has_fulltext":true,"cited_by_count":133,"citation_normalized_percentile":{"value":0.99226466,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"34","issue":"90001","first_page":"D82","last_page":"D85"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11426","display_name":"Genetically Modified Organisms Research","score":0.9603999853134155,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11426","display_name":"Genetically Modified Organisms Research","score":0.9603999853134155,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12929","display_name":"Animal Genetics and Reproduction","score":0.9121000170707703,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.9111663103103638},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4514141380786896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.408976674079895}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9111663103103638},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4514141380786896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.408976674079895}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":"Q000266","qualifier_name":"history","is_major_topic":true},{"descriptor_ui":"D049673","descriptor_name":"History, 20th Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049673","descriptor_name":"History, 20th Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049673","descriptor_name":"History, 20th Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049674","descriptor_name":"History, 21st Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049674","descriptor_name":"History, 21st Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049674","descriptor_name":"History, 21st Century","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkj146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj146","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D82/3926336/gkj146.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381980","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381980","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":"Historical Article"},{"id":"pmh:oai:europepmc.org:156933","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347508","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1347508","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347508","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1021.5865","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1021.5865","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/suppl_1/D82.full.pdf","raw_type":"text"},{"id":"pmh:oai:infoscience.epfl.ch:114912","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/114912","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj146","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D82/3926336/gkj146.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G6224960559","display_name":"New bioinformatics-driven approaches for cancer genomics.","funder_award_id":"104248","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8832621192","display_name":null,"funder_award_id":"3100A0","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134193442.pdf","grobid_xml":"https://content.openalex.org/works/W2134193442.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1917767512","https://openalex.org/W1998364073","https://openalex.org/W2006439752","https://openalex.org/W2015471909","https://openalex.org/W2015502807","https://openalex.org/W2016923471","https://openalex.org/W2032284355","https://openalex.org/W2045319488","https://openalex.org/W2069047984","https://openalex.org/W2071405543","https://openalex.org/W2083479872","https://openalex.org/W2096525273","https://openalex.org/W2097353028","https://openalex.org/W2099468911","https://openalex.org/W2101163218","https://openalex.org/W2101690350","https://openalex.org/W2120761571","https://openalex.org/W2144905501","https://openalex.org/W2145366820","https://openalex.org/W2147305638","https://openalex.org/W2151587693","https://openalex.org/W2153438927","https://openalex.org/W2157215359","https://openalex.org/W2160073543","https://openalex.org/W2164296513","https://openalex.org/W2167272207","https://openalex.org/W2168783124","https://openalex.org/W4213167074","https://openalex.org/W4237781946","https://openalex.org/W4242043490","https://openalex.org/W4245803912","https://openalex.org/W4248160505"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"The":[0,75],"Eukaryotic":[1],"Promoter":[2,37],"Database":[3],"(EPD)":[4],"is":[5,27,81],"an":[6],"annotated":[7],"non-redundant":[8],"collection":[9],"of":[10,59,77,103,111,122,137],"eukaryotic":[11],"POL":[12],"II":[13],"promoters,":[14],"experimentally":[15],"defined":[16],"by":[17,29,145,152],"a":[18,100,123],"transcription":[19],"start":[20],"site":[21],"(TSS).":[22],"Access":[23],"to":[24,31,82],"promoter":[25,60,85,105,138],"sequences":[26,61,139],"provided":[28],"pointers":[30],"positions":[32],"in":[33,148,163],"the":[34,72,153,164],"corresponding":[35],"genomes.":[36],"evidence":[38],"comes":[39],"from":[40,50,53,71],"conventional":[41],"TSS":[42],"mapping":[43],"experiments":[44],"for":[45,87],"individual":[46],"genes,":[47],"or,":[48],"starting":[49],"release":[51,112],"73,":[52],"mass":[54],"genome":[55],"annotation":[56],"projects.":[57],"Subsets":[58],"with":[62,140],"customized":[63],"5'":[64],"and":[65,158],"3'":[66],"extensions":[67],"can":[68,168],"be":[69,169],"downloaded":[70],"EPD":[73,167],"website.":[74],"focus":[76],"current":[78],"development":[79],"efforts":[80],"reach":[83],"complete":[84],"coverage":[86],"important":[88],"model":[89],"organisms":[90],"as":[91,93,110],"soon":[92],"possible.":[94],"To":[95],"speed":[96],"up":[97],"this":[98],"process,":[99,126],"new":[101,127],"class":[102],"preliminary":[104],"entries":[106],"has":[107],"been":[108,131],"introduced":[109],"83,":[113],"which":[114,133],"requires":[115],"less":[116],"stringent":[117],"admission":[118],"criteria.":[119],"As":[120],"part":[121],"continuous":[124],"integration":[125],"web-based":[128],"interfaces":[129],"have":[130],"developed,":[132],"allow":[134],"joint":[135],"analysis":[136],"other":[141],"bioinformatics":[142],"resources":[143],"developed":[144],"our":[146],"group,":[147],"particular":[149],"programs":[150],"offered":[151],"Signal":[154],"Search":[155],"Analysis":[156],"Server,":[157],"gene":[159],"expression":[160],"data":[161],"stored":[162],"CleanEx":[165],"database.":[166],"accessed":[170],"at":[171],"http://www.epd.isb-sib.ch.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":15}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
