{"id":"https://openalex.org/W2031543645","doi":"https://doi.org/10.1093/nar/gkq930","title":"OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011","display_name":"OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011","publication_year":2010,"publication_date":"2010-10-22","ids":{"openalex":"https://openalex.org/W2031543645","doi":"https://doi.org/10.1093/nar/gkq930","mag":"2031543645"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq930","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq930","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkq930","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067477017","display_name":"Robert M. Waterhouse","orcid":"https://orcid.org/0000-0003-4199-9052"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I114457229","display_name":"University of Geneva","ror":"https://ror.org/01swzsf04","country_code":"CH","type":"education","lineage":["https://openalex.org/I114457229"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Robert M. Waterhouse","raw_affiliation_strings":["Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I114457229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029893038","display_name":"Evgeny M. Zdobnov","orcid":"https://orcid.org/0000-0002-5178-1498"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Evgeny M. Zdobnov","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039659389","display_name":"Fredrik Tegenfeldt","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fredrik Tegenfeldt","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100405717","display_name":"Jia Li","orcid":"https://orcid.org/0000-0003-1500-869X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jia Li","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5038335924","display_name":"Evgenia V. Kriventseva","orcid":"https://orcid.org/0000-0003-4835-7562"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Evgenia V. Kriventseva","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5067477017"],"corresponding_institution_ids":["https://openalex.org/I114457229","https://openalex.org/I12708293"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.2694,"has_fulltext":false,"cited_by_count":145,"citation_normalized_percentile":{"value":0.97989601,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"39","issue":"suppl_1","first_page":"D283","last_page":"D288"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9969000220298767,"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"}},{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.9872000217437744,"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/biology","display_name":"Biology","score":0.8866903781890869},{"id":"https://openalex.org/keywords/phyletic-gradualism","display_name":"Phyletic gradualism","score":0.7402815818786621},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6974286437034607},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.6043722629547119},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5824599266052246},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.573275089263916},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5101280808448792},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4729102551937103},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.41171568632125854},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3924407362937927},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3725689649581909}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8866903781890869},{"id":"https://openalex.org/C150078595","wikidata":"https://www.wikidata.org/wiki/Q1158802","display_name":"Phyletic gradualism","level":4,"score":0.7402815818786621},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6974286437034607},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6043722629547119},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5824599266052246},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.573275089263916},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5101280808448792},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4729102551937103},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.41171568632125854},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3924407362937927},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3725689649581909}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/nar/gkq930","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq930","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3013786","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3013786","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq930","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq930","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5299999713897705,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1236321187","https://openalex.org/W1507241016","https://openalex.org/W1586316126","https://openalex.org/W1691715559","https://openalex.org/W1966786019","https://openalex.org/W1973810564","https://openalex.org/W1977027195","https://openalex.org/W1977746661","https://openalex.org/W1990453950","https://openalex.org/W2009234149","https://openalex.org/W2010562878","https://openalex.org/W2028265997","https://openalex.org/W2029833898","https://openalex.org/W2037883697","https://openalex.org/W2044892321","https://openalex.org/W2047253404","https://openalex.org/W2055146666","https://openalex.org/W2058816652","https://openalex.org/W2069492981","https://openalex.org/W2079955869","https://openalex.org/W2082202339","https://openalex.org/W2086948271","https://openalex.org/W2087064593","https://openalex.org/W2093230361","https://openalex.org/W2103150692","https://openalex.org/W2107344829","https://openalex.org/W2108274915","https://openalex.org/W2108366237","https://openalex.org/W2109368213","https://openalex.org/W2113234327","https://openalex.org/W2116423958","https://openalex.org/W2119801041","https://openalex.org/W2120428260","https://openalex.org/W2122977358","https://openalex.org/W2124397449","https://openalex.org/W2125865118","https://openalex.org/W2126045294","https://openalex.org/W2127660113","https://openalex.org/W2129710424","https://openalex.org/W2132023322","https://openalex.org/W2145100181","https://openalex.org/W2153493935","https://openalex.org/W2154380613","https://openalex.org/W2155606054","https://openalex.org/W2159266221","https://openalex.org/W2163965551","https://openalex.org/W2772934464","https://openalex.org/W4211208250","https://openalex.org/W4388253550"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"The":[0,43,126,137],"concept":[1,65],"of":[2,40,46,63,66,81,88,97,101,118,140,148,151,159,186,188,200],"homology":[3],"drives":[4],"speculation":[5],"on":[6],"a":[7,26,37,50,69,145],"gene\u2019s":[8],"function":[9,161],"in":[10,18,92,162],"any":[11],"given":[12],"species":[13,20,28,90,100],"when":[14],"its":[15],"biological":[16],"roles":[17],"other":[19],"are":[21],"characterized.":[22],"With":[23],"reference":[24],"to":[25,57,184],"specific":[27],"radiation":[29,87],"homologous":[30],"relations":[31,122],"define":[32],"orthologs,":[33],"i.e.":[34],"descendants":[35],"from":[36,182,207],"single":[38],"gene":[39,47,152,160,201],"the":[41,54,58,61,64,77,89,107,149],"ancestor.":[42],"large-scale":[44],"delineation":[45],"genealogies":[48,153],"is":[49,204],"challenging":[51],"task,":[52],"and":[53,104,116,121,133,176,196],"numerous":[55],"approaches":[56],"problem":[59],"reflect":[60],"importance":[62],"orthology":[67],"as":[68,171,173],"cornerstone":[70],"for":[71,194],"comparative":[72],"studies.":[73],"Here,":[74],"we":[75],"present":[76],"updated":[78],"OrthoDB":[79,203],"catalog":[80],"eukaryotic":[82,142],"orthologs":[83],"delineated":[84],"at":[85],"each":[86],"phylogeny":[91],"an":[93],"explicitly":[94],"hierarchical":[95],"manner":[96],"over":[98],"100":[99],"vertebrates,":[102,174],"arthropods":[103,175],"fungi":[105,177],"(including":[106],"metazoa":[108],"level).":[109],"New":[110],"database":[111],"features":[112,128],"include":[113],"functional":[114],"annotations,":[115],"quantification":[117],"evolutionary":[119],"divergence":[120,179],"among":[123],"orthologous":[124],"groups.":[125],"interface":[127],"extended":[129],"phyletic":[130],"profile":[131],"querying":[132],"enhanced":[134],"text-based":[135],"searches.":[136],"ever-increasing":[138],"sampling":[139],"sequenced":[141,164],"genomes":[143],"brings":[144],"clearer":[146],"account":[147],"majority":[150],"that":[154],"will":[155,190],"facilitate":[156],"informed":[157],"hypotheses":[158],"newly":[163],"genomes.":[165],"Furthermore,":[166],"uniform":[167],"analysis":[168],"across":[169],"lineages":[170],"different":[172],"with":[178],"levels":[180],"varying":[181],"several":[183],"hundreds":[185],"millions":[187],"years":[189],"provide":[191],"essential":[192],"data":[193],"uncovering":[195],"quantifying":[197],"long-term":[198],"trends":[199],"evolution.":[202],"freely":[205],"accessible":[206],"http://cegg.unige.ch/orthodb.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":18},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":24},{"year":2012,"cited_by_count":21}],"updated_date":"2026-02-25T08:12:03.925757","created_date":"2025-10-10T00:00:00"}