A Unified Anatomy Ontology of the Vertebrate Skeletal System

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

doi:10.1371/journal.pone.0051070

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.

Highlights

In the discipline of comparative morphology [1], phenotypic diversity is described in free text in a variety of ways, including detailed anatomical studies, descriptions of new species, and characters used in phylogenetic analyses
Analysis of Existing Anatomy Ontologies To build a common representation of skeletal anatomy, we surveyed existing representations in the vertebrate subgroup ontologies (Table 1) to determine the various ways that each had classified skeletal elements and to leverage existing work
Some of the most common issues, including varied representations, found in our examination of the anatomy ontologies were as follows: 1) The representation of bone as an organ, i.e., a skeletal element, and bone as a tissue were conflated as was cartilage as an organ and cartilage as a tissue

Summary

Introduction

In the discipline of comparative morphology [1], phenotypic diversity is described in free text in a variety of ways, including detailed anatomical studies, descriptions of new species, and characters used in phylogenetic analyses. It is often difficult to compare phenotypes across taxa because of the different terminologies used in these descriptions. Researchers studying different anatomical regions, different taxa, or working within different biological specialties often have dissimilar terminologies [2]. If phenotypic diversity were represented in a common and computable manner, one would be better able to explore the wealth of data available across a broad range of anatomy, development, and taxa and to relate this information to different domains of biological knowledge such as genomics, comparative embryology, and functional morphology [4,5]. By grappling with phenotypic diversity in a structured and formal way, novel inquiries can be made across organismal phenotypic diversity, including evolved natural phenotypes and the mutant phenotypes of model systems

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