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
- Cypriniformes/embryology*
- Cypriniformes/genetics*
- Embryonic Development
- Phenotype
- Computational Biology/methods
- Biological Evolution*
- Mutation/physiology
- Genomics*
- Body Patterning/genetics
- Body Patterning/physiology*
- Models, Animal
- Zebrafish/embryology
- Zebrafish/genetics
- PubMed
- 17599725 Full text @ J. Exp. Zool. B Mol. Dev. Evol.
Citation
Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. Journal of experimental zoology. Part B, Molecular and developmental evolution. 308(5):655-668.
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
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping