{"id":"https://openalex.org/W2093065714","doi":"https://doi.org/10.1109/bibm.2012.6392677","title":"PhylOnt: A domain-specific ontology for phylogeny analysis","display_name":"PhylOnt: A domain-specific ontology for phylogeny analysis","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2093065714","doi":"https://doi.org/10.1109/bibm.2012.6392677","mag":"2093065714"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2012.6392677","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392677","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://works.bepress.com/amit_sheth/318","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041727019","display_name":"Maryam Panahiazar","orcid":"https://orcid.org/0000-0003-2089-3937"},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]},{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Maryam Panahiazar","raw_affiliation_strings":["Bioinformatics Institute, University of Georgia, Athens, GA, USA","Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, University of Georgia, Athens, GA, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023654056","display_name":"Ajith Ranabahu","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ajith Ranabahu","raw_affiliation_strings":["Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA"],"affiliations":[{"raw_affiliation_string":"Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068171913","display_name":"Vahid Taslimi","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vahid Taslimi","raw_affiliation_strings":["Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA"],"affiliations":[{"raw_affiliation_string":"Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061516429","display_name":"Hima Bindu Yalamanchili","orcid":"https://orcid.org/0000-0003-2426-9496"},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hima Yalamanchili","raw_affiliation_strings":["Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA"],"affiliations":[{"raw_affiliation_string":"Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012113866","display_name":"Arlin Stoltzfus","orcid":"https://orcid.org/0000-0002-0963-1357"},"institutions":[{"id":"https://openalex.org/I4389425230","display_name":"Institute for Bioscience and Biotechnology Research","ror":"https://ror.org/02zs3hb12","country_code":null,"type":"facility","lineage":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I1343035065","https://openalex.org/I4389425230","https://openalex.org/I66946132"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]},{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arlin Stoltzfus","raw_affiliation_strings":["Biochemical Science Division, NIST, Gaithersburg, MD, USA","Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA"],"affiliations":[{"raw_affiliation_string":"Biochemical Science Division, NIST, Gaithersburg, MD, USA","institution_ids":[]},{"raw_affiliation_string":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA","institution_ids":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I66946132","https://openalex.org/I4389425230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055252653","display_name":"Jim Leebens\u2010Mack","orcid":"https://orcid.org/0000-0003-4811-2231"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jim Leebens-Mack","raw_affiliation_strings":["Department of Plant Biology, University of Georgia, Athens, GA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Plant Biology, University of Georgia, Athens, GA, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028772801","display_name":"Amit Sheth","orcid":null},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amit P. Sheth","raw_affiliation_strings":["Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA"],"affiliations":[{"raw_affiliation_string":"Ohio Center for Excellence in Knowledge-enabled Computing (kno.e.sis), College of Computer Science and Engineering, Wright State University, Dayton, OH, USA","institution_ids":["https://openalex.org/I19648265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5041727019"],"corresponding_institution_ids":["https://openalex.org/I165733156","https://openalex.org/I19648265"],"apc_list":null,"apc_paid":null,"fwci":0.2689,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5874211,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"45","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9973999857902527,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9973999857902527,"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":0.9965000152587891,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9797999858856201,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7579815983772278},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6150639057159424},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.586601734161377},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.49533429741859436},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.4741517901420593},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4308621287345886},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.42947983741760254},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4172065556049347},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.34318414330482483},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32962414622306824},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25181150436401367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22445130348205566},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.18887245655059814},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.1815369427204132},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09617111086845398}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7579815983772278},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6150639057159424},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.586601734161377},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.49533429741859436},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4741517901420593},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4308621287345886},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.42947983741760254},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4172065556049347},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.34318414330482483},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32962414622306824},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25181150436401367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22445130348205566},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.18887245655059814},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.1815369427204132},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09617111086845398},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/bibm.2012.6392677","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392677","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},{"id":"pmh:oai:corescholar.libraries.wright.edu:knoesis-1967","is_oa":false,"landing_page_url":"https://corescholar.libraries.wright.edu/knoesis/591","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":false,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Kno.e.sis Publications","raw_type":"text"},{"id":"pmh:oai:scholarcommons.sc.edu:aii_fac_pub-1160","is_oa":false,"landing_page_url":"https://scholarcommons.sc.edu/aii_fac_pub/162","pdf_url":null,"source":{"id":"https://openalex.org/S4306401386","display_name":"Scholar Commons (University of South Carolina)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155781252","host_organization_name":"University of South Carolina","host_organization_lineage":["https://openalex.org/I155781252"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Publications","raw_type":"text"},{"id":"pmh:oai:works.bepress.com:amit_sheth-1317","is_oa":true,"landing_page_url":"https://works.bepress.com/amit_sheth/318","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Amit P. Sheth","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:works.bepress.com:amit_sheth-1317","is_oa":true,"landing_page_url":"https://works.bepress.com/amit_sheth/318","pdf_url":null,"source":{"id":"https://openalex.org/S2737205702","display_name":"Journal of Bioresource Management","issn_l":"2309-3854","issn":["2309-3854"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":"https://openalex.org/P4310316536","host_organization_name":"Bioresource Research Center (BRC), Islamabad","host_organization_lineage":["https://openalex.org/P4310316536"],"host_organization_lineage_names":["Bioresource Research Center (BRC), Islamabad"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Amit P. Sheth","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311400","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43"},{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W766710792","https://openalex.org/W1487781539","https://openalex.org/W1604017289","https://openalex.org/W1948465343","https://openalex.org/W1975957527","https://openalex.org/W2004389753","https://openalex.org/W2073311652","https://openalex.org/W2101846955","https://openalex.org/W2123023543","https://openalex.org/W2135017728","https://openalex.org/W2465309725","https://openalex.org/W6622350143","https://openalex.org/W6636386987"],"related_works":["https://openalex.org/W1506177826","https://openalex.org/W2127299687","https://openalex.org/W2726617685","https://openalex.org/W1794266373","https://openalex.org/W2159818280","https://openalex.org/W22148886","https://openalex.org/W4255991504","https://openalex.org/W2111194626","https://openalex.org/W1562796463","https://openalex.org/W3135477004"],"abstract_inverted_index":{"Phylogenetic":[0],"analyses":[1,65],"can":[2,15,66,215],"resolve":[3],"historical":[4],"relationships":[5,14],"among":[6],"genes,":[7],"organisms":[8],"or":[9,45],"higher":[10],"taxa.":[11],"Understanding":[12],"such":[13],"elucidate":[16],"a":[17,29,130,156],"wide":[18],"range":[19],"of":[20,26,31,35,49,54,56,87,97,105,110,120,137,168,187,202,225],"biological":[21],"phenomena":[22],"including":[23,135,171],"the":[24,33,41,46,85,95,108,118,149,185,200,221],"role":[25],"adaptation":[27],"as":[28],"driver":[30],"diversification,":[32],"importance":[34],"gene":[36,43],"and":[37,58,76,93,107,140,160,166,174,195,223],"genome":[38],"duplications":[39],"in":[40,63,181],"evolution":[42],"function,":[44],"evolutionary":[47],"consequences":[48],"biogeographic":[50],"shifts.":[51],"The":[52,177,212],"variety":[53,96],"methods":[55,104,150],"analysis":[57,106,165],"data":[59,139,157,189],"types":[60,190],"typically":[61],"employed":[62,151],"phylogenetic":[64,102,111,126,164,169,227],"pose":[67],"challenges":[68,80],"for":[69,125,132,163],"semantic":[70,210,213],"reasoning":[71],"due":[72],"to":[73,91,100,152,208],"significant":[74],"representational":[75],"computational":[77],"complexity.":[78],"These":[79],"could":[81],"be":[82],"ameliorated":[83],"with":[84],"development":[86,119],"an":[88,123,144],"ontology":[89,124],"designed":[90],"capture":[92],"organize":[94],"concepts":[98],"used":[99,162],"describe":[101],"data,":[103],"results":[109],"analyses.":[112],"In":[113],"this":[114],"paper,":[115],"we":[116,204],"discuss":[117],"PhylOnt":[121,142,182],"-":[122],"analyses,":[127],"which":[128,147],"establishes":[129],"foundation":[131],"semantics-based":[133],"workflows":[134,218],"meta-analyses":[136],"phylogentic":[138],"trees.":[141],"is":[143],"extensible":[145],"ontology,":[146],"describes":[148],"estimate":[153],"trees":[154,170],"given":[155],"matrix,":[158],"models":[159],"programs":[161],"descriptions":[167],"branch-length":[172],"information":[173],"support":[175,209,217],"values.":[176],"relational":[178],"vocabulary":[179],"included":[180],"will":[183],"facilitate":[184],"integration":[186,224],"heterogeneous":[188,226],"derived":[191],"from":[192],"both":[193],"structured":[194],"unstructured":[196],"sources.":[197],"To":[198],"illustrate":[199],"utility":[201],"PhylOnt,":[203],"annotated":[205],"scientific":[206],"literature":[207],"search.":[211],"annotations":[214],"subsequently":[216],"that":[219],"requiring":[220],"exchange":[222],"information.":[228]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
