Journal article
A Unified Anatomy Ontology of the Vertebrate Skeletal System
PloS one, v 7(12), pp e51070-e51070
10 Dec 2012
PMID: 23251424
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
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Details
- Title
- A Unified Anatomy Ontology of the Vertebrate Skeletal System
- Creators
- Wasila M. Dahdul - University of South DakotaJames P. Balhoff - University of North Carolina at Chapel HillDavid C. Blackburn - California Academy of SciencesAlexander D. Diehl - Jacobs InstituteMelissa A. Haendel - Oregon Health & Science UniversityBrian K. Hall - Dalhousie UniversityHilmar Lapp - National Evolutionary Synthesis CenterJohn G. Lundberg - Drexel UniversityChristopher J. Mungall - Lawrence Berkeley National LaboratoryMartin Ringwald - Jackson LaboratoryErik Segerdell - Oregon Health & Science UniversityCeri E. Van Slyke - University of OregonMatthew K. Vickaryous - University of GuelphMonte Westerfield - University of OregonPaula M. Mabee - University of South DakotaLawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Details
- PloS one, v 7(12), pp e51070-e51070
- Publisher
- Public Library Science
- Number of pages
- 10
- Grant note
- NSF EF-0423641; EF-0905606 / National Evolutionary Synthesis Center 1062542 / Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) HG002659 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA DBI-0641025; DBI-1062404; DBI-1062542 / National Science Foundation; National Science Foundation (NSF) 1062404 / Div Of Biological Infrastructure; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES); Academy of Natural Sciences of Drexel University
- Web of Science ID
- WOS:000312201900038
- Scopus ID
- 2-s2.0-84870877585
- Other Identifier
- 991019335514704721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Genetics & Heredity