{"id":"https://openalex.org/W2167645766","doi":"https://doi.org/10.1093/bib/bbr034","title":"Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees","display_name":"Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees","publication_year":2011,"publication_date":"2011-07-07","ids":{"openalex":"https://openalex.org/W2167645766","doi":"https://doi.org/10.1093/bib/bbr034","mag":"2167645766","pmid":"https://pubmed.ncbi.nlm.nih.gov/21737420"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr034","pdf_url":"https://academic.oup.com/bib/article-pdf/12/5/423/753549/bbr034.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/12/5/423/753549/bbr034.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045485620","display_name":"B. Boeckmann","orcid":null},"institutions":[{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]},{"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"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"B. Boeckmann","raw_affiliation_strings":["Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland. brigitte.boeckmann@isb-sib.ch","Department of Ecology and Evolution in the University of Lausanne,","Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland"],"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland. brigitte.boeckmann@isb-sib.ch","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Ecology and Evolution in the University of Lausanne,","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054250703","display_name":"Marc Robinson\u2010Rechavi","orcid":"https://orcid.org/0000-0002-3437-3329"},"institutions":[{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"M. Robinson-Rechavi","raw_affiliation_strings":["Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","Department of Ecology and Evolution in the University of Lausanne,"],"affiliations":[{"raw_affiliation_string":"Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Department of Ecology and Evolution in the University of Lausanne,","institution_ids":["https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065825020","display_name":"Ioannis X\u00e9narios","orcid":"https://orcid.org/0000-0002-3413-6841"},"institutions":[{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"I. Xenarios","raw_affiliation_strings":["Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","Department of Ecology and Evolution in the University of Lausanne,"],"affiliations":[{"raw_affiliation_string":"Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Department of Ecology and Evolution in the University of Lausanne,","institution_ids":["https://openalex.org/I97565354"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050068380","display_name":"Christophe Dessimoz","orcid":"https://orcid.org/0000-0002-2170-853X"},"institutions":[{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"C. Dessimoz","raw_affiliation_strings":["Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","Department of Ecology and Evolution in the University of Lausanne,"],"affiliations":[{"raw_affiliation_string":"Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Me \u00b4dical Universitaire, 1211 Geneva 4, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Department of Ecology and Evolution in the University of Lausanne,","institution_ids":["https://openalex.org/I97565354"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5045485620"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I97565354"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.668,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.90616751,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"5","first_page":"423","last_page":"435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980999827384949,"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":0.9980999827384949,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9901999831199646,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.8350499868392944},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5766870379447937},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5478271842002869},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4333956837654114},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38387271761894226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32857149839401245},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20655733346939087},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.11457395553588867},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.07418817281723022}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8350499868392944},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5766870379447937},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5478271842002869},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4333956837654114},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38387271761894226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32857149839401245},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20655733346939087},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.11457395553588867},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.07418817281723022}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010865","descriptor_name":"Pilot Projects","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010865","descriptor_name":"Pilot Projects","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010865","descriptor_name":"Pilot Projects","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1093/bib/bbr034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr034","pdf_url":"https://academic.oup.com/bib/article-pdf/12/5/423/753549/bbr034.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21737420","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21737420","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:iris.unil.ch:iris/47544","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/47544","pdf_url":"https://iris.unil.ch/bitstreams/4d546cbd-f84a-4241-9a7a-420d50bb744e/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"journal article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1395185","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1395185/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   BRIEFINGS IN BIOINFORMATICS , 12  (5)   pp. 423-435.   (2011)      ","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3178055","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3178055","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":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:serval.unil.ch:BIB_3EF9A7BDC38C","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_3EF9A7BDC38C","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"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":"Briefings in Bioinformatics, vol. 12, no. 5, pp. 423-435","raw_type":"info:eu-repo/semantics/submittedVersion"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/159704","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/159704","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 12 (5)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000159704","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000159704","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bib/bbr034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr034","pdf_url":"https://academic.oup.com/bib/article-pdf/12/5/423/753549/bbr034.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167645766.pdf","grobid_xml":"https://content.openalex.org/works/W2167645766.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1586941025","https://openalex.org/W1973810564","https://openalex.org/W1996835973","https://openalex.org/W2004798786","https://openalex.org/W2009234149","https://openalex.org/W2013067928","https://openalex.org/W2017519756","https://openalex.org/W2031543645","https://openalex.org/W2045534443","https://openalex.org/W2047253404","https://openalex.org/W2048448217","https://openalex.org/W2060425093","https://openalex.org/W2062018285","https://openalex.org/W2082202339","https://openalex.org/W2082473664","https://openalex.org/W2086015868","https://openalex.org/W2098448352","https://openalex.org/W2100238259","https://openalex.org/W2108366237","https://openalex.org/W2109368213","https://openalex.org/W2111211467","https://openalex.org/W2114250447","https://openalex.org/W2127660113","https://openalex.org/W2132023322","https://openalex.org/W2132926880","https://openalex.org/W2137450588","https://openalex.org/W2140872496","https://openalex.org/W2143335572","https://openalex.org/W2143592941","https://openalex.org/W2146058063","https://openalex.org/W2159266221","https://openalex.org/W2168048337","https://openalex.org/W2170252811","https://openalex.org/W2772934464","https://openalex.org/W4211208250"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W4230315250","https://openalex.org/W2086519370","https://openalex.org/W2087343574"],"abstract_inverted_index":{"Phylogenomic":[0],"databases":[1,20,25,101,141],"provide":[2,112,135],"orthology":[3,54],"predictions":[4],"for":[5,56,76,115,139],"species":[6],"with":[7],"fully":[8,104],"sequenced":[9],"genomes.":[10],"Although":[11],"the":[12,16,37,64,72,77,83,90,100,124,162],"goal":[13],"seems":[14],"well-defined,":[15],"content":[17],"of":[18,39,53,66,99,120,129,161],"these":[19,57],"differs":[21],"greatly.":[22],"Seven":[23],"ortholog":[24],"(Ensembl":[26],"Compara,":[27],"eggNOG,":[28],"HOGENOM,":[29],"InParanoid,":[30],"OMA,":[31],"OrthoDB,":[32],"Panther)":[33],"were":[34],"compared":[35],"on":[36],"basis":[38],"reference":[40],"trees.":[41],"For":[42],"three":[43],"well-conserved":[44],"protein":[45,108],"families,":[46],"we":[47],"observed":[48],"a":[49,103,113,126,136],"generally":[50],"high":[51],"specificity":[52],"assignments":[55],"databases.":[58,122],"We":[59],"show":[60],"that":[61],"differences":[62,88],"in":[63,71,89],"completeness":[65],"predicted":[67],"gene":[68],"relationships":[69],"and":[70,106,117,154],"phylogenetic":[73,132],"information":[74],"are,":[75],"great":[78],"majority,":[79],"not":[80],"due":[81],"to":[82,87,95,142,158],"methods":[84],"used,":[85],"but":[86],"underlying":[91],"database":[92,152],"concepts.":[93],"According":[94],"our":[96],"metrics,":[97],"none":[98],"provides":[102],"correct":[105],"comprehensive":[107],"classification.":[109],"Our":[110],"results":[111],"framework":[114],"meaningful":[116],"systematic":[118],"comparisons":[119],"phylogenomic":[121,140],"In":[123],"future,":[125],"sustainable":[127],"set":[128],"'Gold":[130],"standard'":[131],"trees":[133],"could":[134],"robust":[137],"method":[138],"assess":[143],"their":[144],"current":[145],"quality":[146],"status,":[147],"measure":[148],"changes":[149],"following":[150],"new":[151],"releases":[153],"diagnose":[155],"improvements":[156],"subsequent":[157],"an":[159],"upgrade":[160],"analysis":[163],"procedure.":[164]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
