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The teleost anatomy ontology: anatomical representation for the genomics age.

Publication ,  Journal Article
Dahdul, WM; Lundberg, JG; Midford, PE; Balhoff, JP; Lapp, H; Vision, TJ; Haendel, MA; Westerfield, M; Mabee, PM
Published in: Systematic biology
July 2010

The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.

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Published In

Systematic biology

DOI

EISSN

1076-836X

ISSN

1063-5157

Publication Date

July 2010

Volume

59

Issue

4

Start / End Page

369 / 383

Related Subject Headings

  • Genomics
  • Fishes
  • Evolutionary Biology
  • Databases, Factual
  • Computational Biology
  • Classification
  • Biological Evolution
  • Animals
  • 3105 Genetics
  • 3104 Evolutionary biology
 

Citation

APA
Chicago
ICMJE
MLA
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Dahdul, W. M., Lundberg, J. G., Midford, P. E., Balhoff, J. P., Lapp, H., Vision, T. J., … Mabee, P. M. (2010). The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology, 59(4), 369–383. https://doi.org/10.1093/sysbio/syq013
Dahdul, Wasila M., John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield, and Paula M. Mabee. “The teleost anatomy ontology: anatomical representation for the genomics age.Systematic Biology 59, no. 4 (July 2010): 369–83. https://doi.org/10.1093/sysbio/syq013.
Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, et al. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic biology. 2010 Jul;59(4):369–83.
Dahdul, Wasila M., et al. “The teleost anatomy ontology: anatomical representation for the genomics age.Systematic Biology, vol. 59, no. 4, July 2010, pp. 369–83. Epmc, doi:10.1093/sysbio/syq013.
Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic biology. 2010 Jul;59(4):369–383.
Journal cover image

Published In

Systematic biology

DOI

EISSN

1076-836X

ISSN

1063-5157

Publication Date

July 2010

Volume

59

Issue

4

Start / End Page

369 / 383

Related Subject Headings

  • Genomics
  • Fishes
  • Evolutionary Biology
  • Databases, Factual
  • Computational Biology
  • Classification
  • Biological Evolution
  • Animals
  • 3105 Genetics
  • 3104 Evolutionary biology