Aside from the Evolutionary Biology and Ontologies Workshop that we organize together with the NCBO at the Evolution Meeting 2008 in Minneapolis, we will also be presenting a poster. For your advance pleasure, here is the abstract that we wrote, only to realize that registration for a poster presentation actually did not require or even offer any abstract submission.
Title: Linking evolutionary morphology to genomics using ontologies
Authors: Paula Mabee, Jim Balhoff, Wasila Dahdul, Hilmar Lapp, John Lundberg, Peter Midford, Todd Vision, Monte Westerfield
Although systematists have collected comparative morphological data for decades, it has been rendered in free-form text and is not computable. Even seemingly straightforward comparisons across taxa, such as examining evolutionary patterns of characters from the same body region (e.g. head) or of the same quality (e.g. shape changes), cannot be made broadly without a database and some means of computation. Ontologies, or structured vocabularies with semantically defined relationships, provide such means and facilitate integration with other databases, including genetics databases from model organisms. Using ostariophysan fishes, we are prototyping a system with an ontology-based character database and generalizable tools to integrate evolutionary and model organism phenotype data. This system is designed to meet the top-priority needs of the evolutionary community concerning development and evolution of morphology. These include mapping characters on trees and identification of clades in which traits vary (quick retrieval of character state distributions), correlation matrices of traits, identification of candidate genes, and phenotypic BLAST to discover similar phenotypes and similar OTUs. Such queries will help address large-scale questions about the genetic and developmental regulation of evolutionary morphological transitions.
To date we have laid the groundwork for character annotation through the development of multiple ontologies, curatorial tools, and careful consideration of how to deal with homology, types of evidence, and voucher specimens. We have developed a multi-species anatomy ontology for teleost fishes (Teleost Anatomy Ontology) using the existing zebrafish anatomy ontology as its core. [The TAO is being expanded and refined by the broader ichthyological community]. We have developed new components for Phenote, an open source software application, to facilitate the annotation of evolutionary characters from the literature using terms from the teleost anatomy ontology in combination with terms from the Phenotype and Trait Ontology (PATO) and Spatial Ontology (BSPO), following and adapting the Entity/Quality syntax of model organism databases. New components of Phenote include a phylogeny view for graphically selecting clades to annotate, a taxon list manager for entry of voucher specimen identifiers, a data filtering interface, and more. We are documenting character observations from individual species whose names are drawn from a taxonomy ontology (Teleost Taxonomy Ontology) that we developed based on an expert database, the Catalog of Fishes. Phenoscape will enable researchers to investigate relationships between evolutionary changes in morphology and the phenotypes seen in genetically characterized developmental mutants of zebrafish.