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500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.

Publication ,  Journal Article
Mabee, BP; Balhoff, JP; Dahdul, WM; Lapp, H; Midford, PE; Vision, TJ; Westerfield, M
Published in: Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology
June 2012

The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2,500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery.

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Published In

Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology

DOI

EISSN

1439-0426

ISSN

0175-8659

Publication Date

June 2012

Volume

28

Issue

3

Start / End Page

300 / 305

Related Subject Headings

  • Fisheries
  • 3109 Zoology
  • 3005 Fisheries sciences
  • 0699 Other Biological Sciences
  • 0608 Zoology
 

Citation

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Mabee, B. P., Balhoff, J. P., Dahdul, W. M., Lapp, H., Midford, P. E., Vision, T. J., & Westerfield, M. (2012). 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Zeitschrift Fur Angewandte Ichthyologie = Journal of Applied Ichthyology, 28(3), 300–305. https://doi.org/10.1111/j.1439-0426.2012.01985.x
Mabee, By Paula, James P. Balhoff, Wasila M. Dahdul, Hilmar Lapp, Peter E. Midford, Todd J. Vision, and Monte Westerfield. “500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.Zeitschrift Fur Angewandte Ichthyologie = Journal of Applied Ichthyology 28, no. 3 (June 2012): 300–305. https://doi.org/10.1111/j.1439-0426.2012.01985.x.
Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, et al. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology. 2012 Jun;28(3):300–5.
Mabee, By Paula, et al. “500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.Zeitschrift Fur Angewandte Ichthyologie = Journal of Applied Ichthyology, vol. 28, no. 3, June 2012, pp. 300–05. Epmc, doi:10.1111/j.1439-0426.2012.01985.x.
Mabee BP, Balhoff JP, Dahdul WM, Lapp H, Midford PE, Vision TJ, Westerfield M. 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology. 2012 Jun;28(3):300–305.
Journal cover image

Published In

Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology

DOI

EISSN

1439-0426

ISSN

0175-8659

Publication Date

June 2012

Volume

28

Issue

3

Start / End Page

300 / 305

Related Subject Headings

  • Fisheries
  • 3109 Zoology
  • 3005 Fisheries sciences
  • 0699 Other Biological Sciences
  • 0608 Zoology