The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

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Issue Date
2013-11-22Author
Midford, Peter E.
Dececchi, Thomas Alex
Balhoff, James P.
Dahdul, Wasila M.
Ibrahim, Nizar
Lapp, Hilmar
Lundberg, John G.
Mabee, Paula M.
Sereno, Paul C.
Westerfield, Monte
Vision, Todd J.
Blackburn, David C.
Publisher
BioMed Central
Type
Article
Article Version
Scholarly/refereed, publisher version
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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.
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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
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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.
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Except where otherwise noted, this item's license is described as: 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.