title: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.
abstract: BACKGROUND
  Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.
  
  
  RESULTS
  Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.
  
  
  CONCLUSIONS
  The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. THE ONTOLOGY RELEASE FILES ASSOCIATED WITH THE ONTOLOGY MERGE DESCRIBED IN THIS MANUSCRIPT ARE AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ CURRENT ONTOLOGY RELEASE FILES ARE AVAILABLE ALWAYS AVAILABLE AT: http://purl.obolibrary.org/obo/uberon/releases/
authors.affiliation: Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Haendel
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA ; National Evolutionary Synthesis Center, Durham, NC, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Frederic B
authors.initials: FB
authors.lastname: Bastian
authors.affiliation: Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, CA 94118, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Blackburn
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors.forename: Judith A
authors.initials: JA
authors.lastname: Blake
authors.affiliation: The Zebrafish Model Organism Database, University of Oregon, Eugene, OR 97403, USA.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Bradford
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Aurelie
authors.initials: A
authors.lastname: Comte
authors.affiliation: National Evolutionary Synthesis Center, Durham, NC, USA ; Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
authors.forename: Wasila M
authors.initials: WM
authors.lastname: Dahdul
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Dececchi
authors.affiliation: Department of Oral Biology, University of Illinois-Chicago, Chicago, IL 60612, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Druzinsky
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME 04609, USA.
authors.forename: Terry F
authors.initials: TF
authors.lastname: Hayamizu
authors.affiliation: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Nizar
authors.initials: N
authors.lastname: Ibrahim
authors.affiliation: Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA.
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
authors.forename: Paula M
authors.initials: PM
authors.lastname: Mabee
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Anne
authors.initials: A
authors.lastname: Niknejad
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Marc
authors.initials: M
authors.lastname: Robinson-Rechavi
authors.affiliation: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Sereno
authors.affiliation: Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
keywords: Bio-ontology; Evolutionary biology; Morphological variation; Phenotype; Semantic integration