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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; Vision, Todd J; Blackburn, David C.
Afiliação
  • Midford PE; Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, USA. dblackburn@calacademy.org.
J Biomed Semantics ; 4(1): 34, 2013 Nov 22.
Article em En | MEDLINE | ID: mdl-24267744
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/), 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.

Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2013 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2013 Tipo de documento: Article País de afiliação: Estados Unidos