PUBLICATION

Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish

Authors
Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M.
ID
ZDB-PUB-070711-15
Date
2007
Source
Journal of experimental zoology. Part B, Molecular and developmental evolution   308(5): 655-668 (Journal)
Registered Authors
Haendel, Melissa A., Mabee, Paula M., Westerfield, Monte
Keywords
none
MeSH Terms
  • Animals
  • Biological Evolution*
  • Body Patterning/genetics
  • Body Patterning/physiology*
  • Computational Biology/methods
  • Cypriniformes/embryology*
  • Cypriniformes/genetics*
  • Embryonic Development
  • Genomics*
  • Models, Animal
  • Mutation/physiology
  • Phenotype
  • Zebrafish/embryology
  • Zebrafish/genetics
PubMed
17599725 Full text @ J. Exp. Zool. B Mol. Dev. Evol.
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.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes