The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
dc.contributor.author | Midford, Peter E. | |
dc.contributor.author | Dececchi, Thomas Alex | |
dc.contributor.author | Balhoff, James P. | |
dc.contributor.author | Dahdul, Wasila M. | |
dc.contributor.author | Ibrahim, Nizar | |
dc.contributor.author | Lapp, Hilmar | |
dc.contributor.author | Lundberg, John G. | |
dc.contributor.author | Mabee, Paula M. | |
dc.contributor.author | Sereno, Paul C. | |
dc.contributor.author | Westerfield, Monte | |
dc.contributor.author | Vision, Todd J. | |
dc.contributor.author | Blackburn, David C. | |
dc.date.accessioned | 2014-01-17T22:22:33Z | |
dc.date.available | 2014-01-17T22:22:33Z | |
dc.date.issued | 2013-11-22 | |
dc.identifier.citation | Midford, Peter E, Thomas Alex Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg, et al. 2013. “The Vertebrate Taxonomy Ontology: A Framework for Reasoning across Model Organism and Species Phenotypes.” Journal of Biomedical Semantics 4:34. http://dx.doi.org/10.1186/2041-1480-4-34. | |
dc.identifier.uri | http://hdl.handle.net/1808/12821 | |
dc.description.abstract | Background: 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. Description: 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. Conclusions: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/ webcite), 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. Keywords: Data integration; Evolutionary biology; Paleontology; Taxonomic rank | |
dc.publisher | BioMed Central | |
dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. | |
dc.rights.uri | http://creativecommons.org/licenses/by/2.0 | |
dc.subject | Data-integration | |
dc.subject | Evolutionary-biology | |
dc.subject | Paleontology | |
dc.subject | Taxonomic-rank | |
dc.title | The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes | |
dc.type | Article | |
kusw.kuauthor | Midford, Peter E. | |
kusw.kudepartment | Ecology and Evolutionary Biology | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1186/2041-1480-4-34 | |
dc.identifier.orcid | https://orcid.org/0000-0002-1810-9886 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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