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

Journal of Biomedical Semantics - Tập 4 Số 1 - 2013
Peter E. Midford1,2, T. Alexander Dececchi3, James P. Balhoff4,2, Wasila Dahdul3,2, Nizar Ibrahim5, Hilmar Lapp2, John G. Lundberg6, Paula Mabee3, Paul C. Sereno5, Monte Westerfield7, David C. Blackburn8
1Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA
2National Evolutionary Synthesis Center, Durham, USA
3Department of Biology, University of South Dakota, Vermillion, USA
4Department of Biology, University of North Carolina, North Carolina, USA
5Department of Organismal Biology & Anatomy, University of Chicago, Chicago, USA
6Academy of Natural Sciences, Philadelphia, USA
7Institute of Neuroscience, University of Oregon, Eugene, USA
8Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, USA

Tóm tắt

AbstractBackgroundA 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.DescriptionAs 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.ConclusionsThe 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.

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Journal of Biomedical Semantics

Tập 4 Số 1

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