The teleost anatomy ontology: Anatomical representation for the genomics age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa Haendel, Monte Westerfield, Paula M. Mabee

Research output: Contribution to journalArticle

63 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)369-383
Number of pages15
JournalSystematic Biology
Volume59
Issue number4
DOIs
StatePublished - 2010

Fingerprint

Genomics
teleost
Danio rerio
anatomy
Anatomy
genomics
organisms
prototypes
Zebrafish
linkage (genetics)
phenotype
Databases
phylogeny
fish
Genetic Databases
Knowledge Bases
Fishes
phylogenetics
Phenotype

Keywords

  • Bioinformatics
  • Devo-evo
  • Fish
  • Morphology
  • Ontology
  • Teleostei

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Medicine(all)

Cite this

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

The teleost anatomy ontology : Anatomical representation for the genomics age. / Dahdul, Wasila M.; Lundberg, John G.; Midford, Peter E.; Balhoff, James P.; Lapp, Hilmar; Vision, Todd J.; Haendel, Melissa; Westerfield, Monte; Mabee, Paula M.

In: Systematic Biology, Vol. 59, No. 4, 2010, p. 369-383.

Research output: Contribution to journalArticle

Dahdul, WM, Lundberg, JG, Midford, PE, Balhoff, JP, Lapp, H, Vision, TJ, Haendel, M, Westerfield, M & Mabee, PM 2010, 'The teleost anatomy ontology: Anatomical representation for the genomics age', Systematic Biology, vol. 59, no. 4, pp. 369-383. 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;59(4):369-383. https://doi.org/10.1093/sysbio/syq013
Dahdul, Wasila M. ; Lundberg, John G. ; Midford, Peter E. ; Balhoff, James P. ; Lapp, Hilmar ; Vision, Todd J. ; Haendel, Melissa ; Westerfield, Monte ; Mabee, Paula M. / The teleost anatomy ontology : Anatomical representation for the genomics age. In: Systematic Biology. 2010 ; Vol. 59, No. 4. pp. 369-383.
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