{"id":"https://openalex.org/W2152100019","doi":"https://doi.org/10.1093/bioinformatics/btp191","title":"Toward a gold standard for promoter prediction evaluation","display_name":"Toward a gold standard for promoter prediction evaluation","publication_year":2009,"publication_date":"2009-05-27","ids":{"openalex":"https://openalex.org/W2152100019","doi":"https://doi.org/10.1093/bioinformatics/btp191","mag":"2152100019","pmid":"https://pubmed.ncbi.nlm.nih.gov/19478005"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp191","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i313/48991115/bioinformatics_25_12_i313.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i313/48991115/bioinformatics_25_12_i313.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002088014","display_name":"Thomas Abeel","orcid":"https://orcid.org/0000-0002-7205-7431"},"institutions":[{"id":"https://openalex.org/I4210098178","display_name":"VIB-UGent Center for Plant Systems Biology","ror":"https://ror.org/01qnqmc89","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I32597200","https://openalex.org/I4210098178"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Thomas Abeel","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium","institution_ids":["https://openalex.org/I4210098178","https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070738091","display_name":"Yves Van de Peer","orcid":"https://orcid.org/0000-0003-4327-3730"},"institutions":[{"id":"https://openalex.org/I4210098178","display_name":"VIB-UGent Center for Plant Systems Biology","ror":"https://ror.org/01qnqmc89","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I32597200","https://openalex.org/I4210098178"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Yves Van de Peer","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium","institution_ids":["https://openalex.org/I4210098178","https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001585713","display_name":"Yvan Saeys","orcid":"https://orcid.org/0000-0002-0415-1506"},"institutions":[{"id":"https://openalex.org/I4210098178","display_name":"VIB-UGent Center for Plant Systems Biology","ror":"https://ror.org/01qnqmc89","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I32597200","https://openalex.org/I4210098178"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Yvan Saeys","raw_affiliation_strings":["1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium"],"affiliations":[{"raw_affiliation_string":"1 Department of Plant Systems Biology, VIB and 2Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium","institution_ids":["https://openalex.org/I4210098178","https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002088014"],"corresponding_institution_ids":["https://openalex.org/I32597200","https://openalex.org/I4210098178"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.1223,"has_fulltext":true,"cited_by_count":92,"citation_normalized_percentile":{"value":0.96325828,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"25","issue":"12","first_page":"i313","last_page":"i320"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9879999756813049,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},{"id":"https://openalex.org/T10494","display_name":"Plant Virus Research Studies","score":0.9821000099182129,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7643341422080994},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6801618337631226},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6781635284423828},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5793358087539673},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5222126841545105},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4875625967979431},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.45713505148887634},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4359918236732483},{"id":"https://openalex.org/keywords/gold-standard","display_name":"Gold standard (test)","score":0.4140858054161072},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40864497423171997},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29388338327407837},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.22716552019119263},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1596594750881195},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15752500295639038},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12047052383422852},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10786116123199463},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10515293478965759},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.10020577907562256},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07959330081939697},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.06636157631874084}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7643341422080994},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6801618337631226},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6781635284423828},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5793358087539673},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5222126841545105},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4875625967979431},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.45713505148887634},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4359918236732483},{"id":"https://openalex.org/C40993552","wikidata":"https://www.wikidata.org/wiki/Q514654","display_name":"Gold standard (test)","level":2,"score":0.4140858054161072},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40864497423171997},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29388338327407837},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.22716552019119263},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1596594750881195},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15752500295639038},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12047052383422852},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10786116123199463},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10515293478965759},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.10020577907562256},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07959330081939697},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.06636157631874084},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp191","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i313/48991115/bioinformatics_25_12_i313.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19478005","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19478005","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:archive.ugent.be:697733","is_oa":true,"landing_page_url":"http://hdl.handle.net/1854/LU-697733","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:europepmc.org:1855977","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2687945","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp191","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/12/i313/48991115/bioinformatics_25_12_i313.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.550000011920929}],"awards":[{"id":"https://openalex.org/G1638137056","display_name":null,"funder_award_id":"FWO-Vl","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G6867476589","display_name":null,"funder_award_id":"FWO-Vlaanderen","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152100019.pdf","grobid_xml":"https://content.openalex.org/works/W2152100019.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1589930635","https://openalex.org/W1972875048","https://openalex.org/W2003463914","https://openalex.org/W2007142561","https://openalex.org/W2019462186","https://openalex.org/W2057216430","https://openalex.org/W2057692691","https://openalex.org/W2064390432","https://openalex.org/W2070510621","https://openalex.org/W2075435641","https://openalex.org/W2075793022","https://openalex.org/W2093387961","https://openalex.org/W2096329971","https://openalex.org/W2099961908","https://openalex.org/W2105089812","https://openalex.org/W2111400482","https://openalex.org/W2113197426","https://openalex.org/W2114703458","https://openalex.org/W2115992869","https://openalex.org/W2130919037","https://openalex.org/W2148503087","https://openalex.org/W2153392439","https://openalex.org/W2161399316","https://openalex.org/W2164800096","https://openalex.org/W2169351355","https://openalex.org/W6673508764"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2011676020","https://openalex.org/W2000169967"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2021,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":10}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}