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XB-ART-46399
PLoS One. January 1, 2012; 7 (12): e51070.

A unified anatomy ontology of the vertebrate skeletal system.

Dahdul WM , Balhoff JP , Blackburn DC , Diehl AD , Haendel MA , Hall BK , Lapp H , Lundberg JG , Mungall CJ , Ringwald M , Segerdell E , Van Slyke CE , Vickaryous MK , Westerfield M , Mabee PM .


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.

PubMed ID: 23251424
PMC ID: PMC3519498
Article link: PLoS One.
Grant support: HG002659 NHGRI NIH HHS

Genes referenced: act3
Antibodies referenced:
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