{"refrec":{"BRefID":288359,"RR":"<b>Midford, P.E.; Dececchi, T.; Balhoff, J.P.; Dahdul, W.M.; Ibrahim, N.; Lapp, H.; Lundberg, J.G.; Mabee, P.M.; Sereno, P.C.; Westerfield, M.; Vision, T.J.; Blackburn, D.C.</b> (2013). The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. <i>Journal of Biomedical Semantics 4(1)</i>: 34. <a href=\"https://dx.doi.org/10.1186/2041-1480-4-34\" target=\"_blank\">https://dx.doi.org/10.1186/2041-1480-4-34</a>","BEntID":280392,"PublicFlag":1,"CheckedFlag":1,"wosflag":1,"vabbflag":1,"RefStringPartII":". <i>Journal of Biomedical Semantics 4(1)</i>: 34. <a href=\"https://dx.doi.org/10.1186/2041-1480-4-34\" target=\"_blank\">https://dx.doi.org/10.1186/2041-1480-4-34</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Midford, P.E.; Dececchi, T.; Balhoff, J.P.; Dahdul, W.M.; Ibrahim, N.; Lapp, H.; Lundberg, J.G.; Mabee, P.M.; Sereno, P.C.; Westerfield, M.; Vision, T.J.; Blackburn, D.C.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Midford, P.E. <i>et al.</i>","Englishabstract":"A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2024-12-10 01:33:17.368041","timezone_type":1,"timezone":"+01:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":"Data integration, Evolutionary biology, Paleontology, Taxonomic rank","OtherDescriptors":null,"Notes":null,"AnaPub":2013,"MonPub":null,"DateUpdate":"2018-02-13","DateCreate":"2017-08-21","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:000343706500002","VABBcode":null,"OpenAcc":1,"DOI":"10.1186/2041-1480-4-34"},"refs":null,"anarec":{"AnaID":288359,"PubliDate":2013,"Pagination":"34","XtraPublOfAnaID":null,"ISBN":null,"Volume":"4","Issue":"1","BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":271384,"SerRR":"Journal of Biomedical Semantics. 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