title: Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish.
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.
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA. pmabee@usd.edu
authors.forename: Paula M
authors.initials: PM
authors.lastname: Mabee
authors.forename: Gloria
authors.initials: G
authors.lastname: Arratia
authors.forename: Miles
authors.initials: M
authors.lastname: Coburn
authors.forename: Melissa
authors.initials: M
authors.lastname: Haendel
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Hilton
authors.forename: John G
authors.initials: JG
authors.lastname: Lundberg
authors.forename: Richard L
authors.initials: RL
authors.lastname: Mayden
authors.forename: Nelson
authors.initials: N
authors.lastname: Rios
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfield
mesh_terms: D000818:Animals; D005075:Biological Evolution; D019521:Body Patterning / Q000235:genetics / Q000502:physiology*; D019295:Computational Biology / Q000379:methods; D003531:Cypriniformes / Q000196:embryology* / Q000235:genetics*; D047108:Embryonic Development; D023281:Genomics; D023421:Models, Animal; D009154:Mutation / Q000502:physiology; D010641:Phenotype; D015027:Zebrafish / Q000196:embryology / Q000235:genetics