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Title: A Unified Anatomy Ontology of the Vertebrate Skeletal System

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 ofmore » phenotypic diversity« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [5];  [11];  [12];  [11];  [13]
  1. University of South Dakota, Vermillion, SD (United States); National Evolutionary Synthesis Center, Durham, NC (United States)
  2. National Evolutionary Synthesis Center, Durham, NC (United States); University of North Carolina, Chapel Hill, NC (United States)
  3. California Academy of Sciences, San Francisco, CA (United States)
  4. University at Buffalo, NY (United States)
  5. Oregon Health and Science University, Portland, OR (United States)
  6. Dalhousie University, Halifax, NS (United States)
  7. National Evolutionary Synthesis Center, Durham, NC (United States)
  8. The Academy of Natural Sciences, Philadelphia, PA (United States)
  9. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Genomics Division
  10. The Jackson Laboratory, Bar Harbor, ME (United States)
  11. University of Oregon, Eugene, OR (United States)
  12. University of Guelph, ON (Canada)
  13. University of South Dakota, Vermillion, SD (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); National Institutes of Health (NIH); National Evolutionary Synthesis Center
OSTI Identifier:
1627566
Grant/Contract Number:  
AC02-05CH11231; DBI-0641025; DBI-1062404; DBI-1062542; HG002659; EF-0423641; EF-0905606
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 7; Journal Issue: 12; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; animal anatomy; vertebrates; animal musculoskeletal anatomy; comparative anatomy; skeleton; gene ontologies; bone; phenotypes

Citation Formats

Dahdul, Wasila M., Balhoff, James P., Blackburn, David C., Diehl, Alexander D., Haendel, Melissa A., Hall, Brian K., Lapp, Hilmar, Lundberg, John G., Mungall, Christopher J., Ringwald, Martin, Segerdell, Erik, Van Slyke, Ceri E., Vickaryous, Matthew K., Westerfield, Monte, and Mabee, Paula M. A Unified Anatomy Ontology of the Vertebrate Skeletal System. United States: N. p., 2012. Web. doi:10.1371/journal.pone.0051070.
Dahdul, Wasila M., Balhoff, James P., Blackburn, David C., Diehl, Alexander D., Haendel, Melissa A., Hall, Brian K., Lapp, Hilmar, Lundberg, John G., Mungall, Christopher J., Ringwald, Martin, Segerdell, Erik, Van Slyke, Ceri E., Vickaryous, Matthew K., Westerfield, Monte, & Mabee, Paula M. A Unified Anatomy Ontology of the Vertebrate Skeletal System. United States. https://doi.org/10.1371/journal.pone.0051070
Dahdul, Wasila M., Balhoff, James P., Blackburn, David C., Diehl, Alexander D., Haendel, Melissa A., Hall, Brian K., Lapp, Hilmar, Lundberg, John G., Mungall, Christopher J., Ringwald, Martin, Segerdell, Erik, Van Slyke, Ceri E., Vickaryous, Matthew K., Westerfield, Monte, and Mabee, Paula M. Mon . "A Unified Anatomy Ontology of the Vertebrate Skeletal System". United States. https://doi.org/10.1371/journal.pone.0051070. https://www.osti.gov/servlets/purl/1627566.
@article{osti_1627566,
title = {A Unified Anatomy Ontology of the Vertebrate Skeletal System},
author = {Dahdul, Wasila M. and Balhoff, James P. and Blackburn, David C. and Diehl, Alexander D. and Haendel, Melissa A. and Hall, Brian K. and Lapp, Hilmar and Lundberg, John G. and Mungall, Christopher J. and Ringwald, Martin and Segerdell, Erik and Van Slyke, Ceri E. and Vickaryous, Matthew K. and Westerfield, Monte and Mabee, Paula M.},
abstractNote = {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},
doi = {10.1371/journal.pone.0051070},
journal = {PLoS ONE},
number = 12,
volume = 7,
place = {United States},
year = {Mon Dec 10 00:00:00 EST 2012},
month = {Mon Dec 10 00:00:00 EST 2012}
}

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