{"id":"https://openalex.org/W2552792806","doi":"https://doi.org/10.1186/s12859-016-1267-3","title":"On the consistency of orthology relationships","display_name":"On the consistency of orthology relationships","publication_year":2016,"publication_date":"2016-11-01","ids":{"openalex":"https://openalex.org/W2552792806","doi":"https://doi.org/10.1186/s12859-016-1267-3","mag":"2552792806","pmid":"https://pubmed.ncbi.nlm.nih.gov/28185580"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1267-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1267-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1267-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1267-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091128796","display_name":"Mark Jones","orcid":"https://orcid.org/0000-0002-4091-7089"},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210101743","display_name":"Laboratoire d'Informatique, de Robotique et de Micro\u00e9lectronique de Montpellier","ror":"https://ror.org/013yean28","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I151295451","https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I4210159245","https://openalex.org/I4412460525"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mark Jones","raw_affiliation_strings":["LIRMM, CNRS, Universit\u00e9 de Montpellier, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"LIRMM, CNRS, Universit\u00e9 de Montpellier, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210101743","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028652077","display_name":"Christophe Paul","orcid":"https://orcid.org/0000-0001-6519-975X"},"institutions":[{"id":"https://openalex.org/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christophe Paul","raw_affiliation_strings":["ISE-M, CNRS, IRD, EPHE, Universit\u00e9, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"ISE-M, CNRS, IRD, EPHE, Universit\u00e9, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I159885104","https://openalex.org/I4210166444","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057284934","display_name":"C\u00e9line Scornavacca","orcid":"https://orcid.org/0009-0004-0179-9771"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"C\u00e9line Scornavacca","raw_affiliation_strings":["ISE-M, CNRS, IRD, EPHE, Universit\u00e9, Montpellier, France. celine.scornavacca@umontpellier.fr","ISE-M, CNRS, IRD, EPHE, Universit\u00e9, Montpellier, France"],"affiliations":[{"raw_affiliation_string":"ISE-M, CNRS, IRD, EPHE, Universit\u00e9, Montpellier, France. celine.scornavacca@umontpellier.fr","institution_ids":[]},{"raw_affiliation_string":"ISE-M, CNRS, IRD, EPHE, Universit\u00e9, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I159885104","https://openalex.org/I4210166444","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057284934"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I4210166444"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5229,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.7267812,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"17","issue":"S14","first_page":"416","last_page":"416"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9980000257492065,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.7014079689979553},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6566016674041748},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.582193911075592},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5621330738067627},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.48361435532569885},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4831809103488922},{"id":"https://openalex.org/keywords/polynomial","display_name":"Polynomial","score":0.4380108416080475},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.43091168999671936},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40682676434516907},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33935070037841797},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3160855174064636},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.22364920377731323},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17393290996551514},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11833038926124573}],"concepts":[{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.7014079689979553},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6566016674041748},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.582193911075592},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5621330738067627},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.48361435532569885},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4831809103488922},{"id":"https://openalex.org/C90119067","wikidata":"https://www.wikidata.org/wiki/Q43260","display_name":"Polynomial","level":2,"score":0.4380108416080475},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.43091168999671936},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40682676434516907},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33935070037841797},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3160855174064636},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.22364920377731323},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17393290996551514},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11833038926124573},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-016-1267-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1267-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1267-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28185580","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28185580","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:HAL:lirmm-01481206v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-01481206","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2016, 17 (S14), pp.11-14. &#x27E8;10.1186/s12859-016-1267-3&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:5123252","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5123252","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1267-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1267-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-016-1267-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1514226263","display_name":null,"funder_award_id":"ANR-10-LABX-20","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5218715900","display_name":null,"funder_award_id":"10-LABX-20","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5549440890","display_name":null,"funder_award_id":"ANR-10-LAB","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G7240651115","display_name":null,"funder_award_id":"ANR-10","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2552792806.pdf","grobid_xml":"https://content.openalex.org/works/W2552792806.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1552559843","https://openalex.org/W1575387405","https://openalex.org/W1931647778","https://openalex.org/W1972157500","https://openalex.org/W1979835060","https://openalex.org/W1992296962","https://openalex.org/W1997093937","https://openalex.org/W2000138132","https://openalex.org/W2008856488","https://openalex.org/W2011039300","https://openalex.org/W2015906942","https://openalex.org/W2022221380","https://openalex.org/W2028775537","https://openalex.org/W2029095423","https://openalex.org/W2032299129","https://openalex.org/W2041346050","https://openalex.org/W2078109763","https://openalex.org/W2101797035","https://openalex.org/W2121654623","https://openalex.org/W2145100181","https://openalex.org/W2149049580","https://openalex.org/W2159266221","https://openalex.org/W2165228561","https://openalex.org/W2166106146","https://openalex.org/W2610183793","https://openalex.org/W2913688336","https://openalex.org/W3210308821","https://openalex.org/W4210290733","https://openalex.org/W4292230561"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W4285822516","https://openalex.org/W1774334694"],"abstract_inverted_index":{"Our":[0],"polynomial":[1],"algorithm":[2],"for":[3],"checking":[4],"consistency":[5],"has":[6],"been":[7],"implemented":[8],"in":[9],"Python":[10],"and":[11],"is":[12],"available":[13],"at":[14],"https://github.com/UdeM-LBIT/OrthoPara-ConstraintChecker":[15],".":[16]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
