A Unified Anatomy Ontology of the Vertebrate Skeletal System

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. van Slyke, Matthew K. Vickaryous, Monte Westerfield, Paula M. Mabee

Research output: Contribution to journalArticle

31 Scopus citations

Abstract

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

Original languageEnglish (US)
Article numbere51070
JournalPloS one
Volume7
Issue number12
DOIs
StatePublished - Dec 10 2012

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Dahdul, W. M., Balhoff, J. P., Blackburn, D. C., Diehl, A. D., Haendel, M. A., Hall, B. K., Lapp, H., Lundberg, J. G., Mungall, C. J., Ringwald, M., Segerdell, E., van Slyke, C. E., Vickaryous, M. K., Westerfield, M., & Mabee, P. M. (2012). A Unified Anatomy Ontology of the Vertebrate Skeletal System. PloS one, 7(12), [e51070]. https://doi.org/10.1371/journal.pone.0051070