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
2007 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
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
more » ... 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. EQ-Entity-Quality syntax where a quality (from PATO) consists of an attribute and a value http://www.bioontology.org/wiki/ index.php/PATO:About FlyBase-Model organism database for Drosophila http://flybase.bio.indiana.edu/ GO-Gene Ontology, developed by a consortium of model organism databases for annotating gene products http://www.geneontology.org/ MGI-Model organism database for mouse (Mouse Genome Informatics) http://www.informatics.jax.org/ OBO-Open Biomedical Ontologies http://obo.sourceforge.net/ browse.html OBO Relations Ontology http://www.obofoundry.org/ro/ PATO-Phenotype and Trait Ontology, an ontology of qualities that are applicable to any organism http://www.bioontology.org/wiki/ index.php/PATO: Main_Page ZFIN-Zebrafish Information Network, the model organism database for zebrafish http://www.zfin.org/ P. M. MABEE ET AL. 656
doi:10.1002/jez.b.21181 pmid:17599725 fatcat:g3zxqegl2jherodstnvyfo2kwm