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The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
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 ... show 2 more
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
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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
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Date
2013-11-22
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BioMed Central
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Keywords
Data-integration, Evolutionary-biology, Paleontology, Taxonomic-rank
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.