{"id":"https://openalex.org/W2160794724","doi":"https://doi.org/10.1093/nar/gkq1090","title":"ODB: a database for operon organizations, 2011 update","display_name":"ODB: a database for operon organizations, 2011 update","publication_year":2010,"publication_date":"2010-11-04","ids":{"openalex":"https://openalex.org/W2160794724","doi":"https://doi.org/10.1093/nar/gkq1090","mag":"2160794724","pmid":"https://pubmed.ncbi.nlm.nih.gov/21051344"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq1090","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq1090","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_1/D552/7628337/gkq1090.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/39/suppl_1/D552/7628337/gkq1090.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062655330","display_name":"Shujiro Okuda","orcid":"https://orcid.org/0000-0002-7704-8104"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]},{"id":"https://openalex.org/I922474255","display_name":"Tokushima University","ror":"https://ror.org/044vy1d05","country_code":"JP","type":"education","lineage":["https://openalex.org/I922474255"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"S. Okuda","raw_affiliation_strings":["College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan. okd@sk.ritsumei.ac.jp","College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577 and 2 Institute for Enzyme Research, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan"],"affiliations":[{"raw_affiliation_string":"College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan. okd@sk.ritsumei.ac.jp","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577 and 2 Institute for Enzyme Research, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan","institution_ids":["https://openalex.org/I922474255","https://openalex.org/I135768898"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001540272","display_name":"Akiyasu C. Yoshizawa","orcid":"https://orcid.org/0000-0002-0870-5502"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]},{"id":"https://openalex.org/I922474255","display_name":"Tokushima University","ror":"https://ror.org/044vy1d05","country_code":"JP","type":"education","lineage":["https://openalex.org/I922474255"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"A. C. Yoshizawa","raw_affiliation_strings":["Institute for Enzyme Research, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan","College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577 and 2 Institute for Enzyme Research, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan"],"affiliations":[{"raw_affiliation_string":"Institute for Enzyme Research, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan","institution_ids":["https://openalex.org/I922474255"]},{"raw_affiliation_string":"College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577 and 2 Institute for Enzyme Research, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan","institution_ids":["https://openalex.org/I922474255","https://openalex.org/I135768898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062655330"],"corresponding_institution_ids":["https://openalex.org/I135768898","https://openalex.org/I922474255"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8132,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.72580191,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"Database","first_page":"D552","last_page":"D555"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9883999824523926,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9883999824523926,"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/T11162","display_name":"Enzyme Structure and Function","score":0.982200026512146,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9761999845504761,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.9481977224349976},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7927647829055786},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6442294716835022},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.45667219161987305},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44258520007133484},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43444138765335083},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.32288554310798645},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2404232919216156}],"concepts":[{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.9481977224349976},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7927647829055786},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6442294716835022},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45667219161987305},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44258520007133484},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43444138765335083},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.32288554310798645},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2404232919216156},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkq1090","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq1090","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_1/D552/7628337/gkq1090.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:21051344","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21051344","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:3013687","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3013687","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq1090","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq1090","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_1/D552/7628337/gkq1090.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":[],"awards":[{"id":"https://openalex.org/G6267471473","display_name":null,"funder_award_id":"Grant-in-Aid","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7693551792","display_name":null,"funder_award_id":"(MEXT)","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160794724.pdf","grobid_xml":"https://content.openalex.org/works/W2160794724.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1966786968","https://openalex.org/W1968698890","https://openalex.org/W2058588742","https://openalex.org/W2062896692","https://openalex.org/W2064384066","https://openalex.org/W2070063001","https://openalex.org/W2078739770","https://openalex.org/W2084902262","https://openalex.org/W2101292724","https://openalex.org/W2114446330","https://openalex.org/W2121564430","https://openalex.org/W2127057035","https://openalex.org/W2144795887","https://openalex.org/W2148973980","https://openalex.org/W2153992812","https://openalex.org/W2155649413","https://openalex.org/W2165335121","https://openalex.org/W2166406784","https://openalex.org/W2171437346"],"related_works":["https://openalex.org/W1608194938","https://openalex.org/W2572774164","https://openalex.org/W1964685767","https://openalex.org/W2111346700","https://openalex.org/W1985756322","https://openalex.org/W2061086355","https://openalex.org/W1541592150","https://openalex.org/W2741414450","https://openalex.org/W2987420353","https://openalex.org/W1491897707"],"abstract_inverted_index":{"ODB":[0,49,98,153,191],"(Operon":[1],"DataBase)":[2],"aims":[3],"to":[4,146],"collect":[5],"data":[6],"of":[7,21,39,60,69,102,116,133,142,164,175,190],"all":[8,127],"known":[9,77,128,134],"and":[10,41,48,63,84],"conserved":[11,88],"operons":[12,33,78,89,104,177],"in":[13,79,167,178],"completely":[14],"sequenced":[15],"genomes.":[16,96,169],"Three":[17],"newly":[18],"updated":[19,188],"features":[20],"this":[22],"database":[23,71],"have":[24],"been":[25],"added":[26,139],"as":[27,105],"follows:":[28],"(i)":[29],"Data":[30],"from":[31,74,91,182],"included":[32],"were":[34],"updated.":[35],"The":[36,66,170,186],"genome-wide":[37,57,140],"analysis":[38,141],"transcription":[40],"transcriptional":[42,58],"units":[43,59],"has":[44],"become":[45],"popular":[46],"recently":[47,138],"successfully":[50],"integrates":[51],"these":[52],"high-throughput":[53],"operon":[54,108,165],"data,":[55],"including":[56,136],"five":[61],"prokaryotes":[62],"two":[64],"eukaryotes.":[65],"current":[67],"version":[68,189],"our":[70],"contains":[72],"information":[73],"about":[75],"10,000":[76],"more":[80,85,92,148],"than":[81,86,93],"50":[82],"genomes,":[83],"400,000":[87],"obtained":[90,181],"1000":[94],"bacterial":[95],"(ii)":[97],"proposes":[99],"the":[100,137,183],"idea":[101],"reference":[103,112,150,184],"a":[106,114],"new":[107,156],"prediction":[109],"tool.":[110],"A":[111,130],"operon,":[113],"set":[115],"possible":[117,176],"orthologous":[118],"genes":[119],"that":[120],"organize":[121],"operons,":[122,135,143],"is":[123,160,172,192],"defined":[124],"by":[125],"clustering":[126],"operons.":[129,151,185],"large":[131],"number":[132],"allowed":[144],"us":[145],"define":[147],"reliable":[149],"(iii)":[152],"also":[154],"provides":[155],"graphical":[157],"interfaces.":[158],"One":[159],"for":[161,173],"comparative":[162],"analyses":[163],"structures":[166],"multiple":[168,179],"other":[171],"visualization":[174],"genomes":[180],"2011":[187],"now":[193],"available":[194],"at":[195],"http://operondb.jp/.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
