Connecting evolutionary morphology to genomics using ontologies: A case study from cypriniformes including zebrafish

Paula M. Mabee, Gloria Arratia, Miles Coburn, Melissa Haendel, Eric J. Hilton, John G. Lundberg, Richard L. Mayden, Nelson Rios, Monte Westerfield

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

One focus of developmental biology is to understand how genes regulate development, and therefore examining the phenotypic effects of gene mutation is a major emphasis in studies of zebrafish and other model organisms. Genetic change underlies alterations in evolutionary characters, or phenotype, and morphological phylogenies inferred by comparison of these characters. We will utilize both existing and new ontologies to connect the evolutionary anatomy and image database that is being developed in the Cypriniformes Tree of Life project to the Zebrafish Information Network (HYPERLINK "file://localhost/ Library/Local%20Settings/Temp/zfin.org" zfin.org) database. Ontologies are controlled vocabularies that formally represent hierarchical relationships among defined biological concepts. If used to recode the free-form text descriptors of anatomical characters, evolutionary character data can become more easily computed, explored, and mined. A shared ontology for homologous modules of the phenotype must be referenced to connect the growing databases in each area in a way that evolutionary questions can be addressed. We present examples that demonstrate the broad utility of this approach.

Original languageEnglish (US)
Pages (from-to)665-668
Number of pages4
JournalJournal of Experimental Zoology Part B: Molecular and Developmental Evolution
Volume308
Issue number5
DOIs
StatePublished - Sep 15 2007
Externally publishedYes

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Cypriniformes
Zebrafish
Genomics
Danio rerio
genomics
Databases
case studies
phenotype
Controlled Vocabulary
information networks
developmental biology
Phenotype
Developmental Biology
Information Services
gene
Phylogeny
anatomy
Genes
Libraries
mutation

ASJC Scopus subject areas

  • Animal Science and Zoology

Cite this

Connecting evolutionary morphology to genomics using ontologies : A case study from cypriniformes including zebrafish. / Mabee, Paula M.; Arratia, Gloria; Coburn, Miles; Haendel, Melissa; Hilton, Eric J.; Lundberg, John G.; Mayden, Richard L.; Rios, Nelson; Westerfield, Monte.

In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Vol. 308, No. 5, 15.09.2007, p. 665-668.

Research output: Contribution to journalArticle

Mabee, Paula M. ; Arratia, Gloria ; Coburn, Miles ; Haendel, Melissa ; Hilton, Eric J. ; Lundberg, John G. ; Mayden, Richard L. ; Rios, Nelson ; Westerfield, Monte. / Connecting evolutionary morphology to genomics using ontologies : A case study from cypriniformes including zebrafish. In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2007 ; Vol. 308, No. 5. pp. 665-668.
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