title: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.
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.
  
  
  METHODS
  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.
authors.affiliation: Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California, USA. dblackburn@calacademy.org.
authors.forename: Peter E
authors.initials: PE
authors.lastname: Midford
authors.forename: Thomas Alex
authors.initials: TA
authors.lastname: Dececchi
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.forename: Wasila M
authors.initials: WM
authors.lastname: Dahdul
authors.forename: Nizar
authors.initials: N
authors.lastname: Ibrahim
authors.forename: Hilmar
authors.initials: H
authors.lastname: Lapp
authors.forename: John G
authors.initials: JG
authors.lastname: Lundberg
authors.forename: Paula M
authors.initials: PM
authors.lastname: Mabee
authors.forename: Paul C
authors.initials: PC
authors.lastname: Sereno
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfield
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Vision
authors.forename: David C
authors.initials: DC
authors.lastname: Blackburn