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Alignment of phenotype ontologies

PI(s): Peter E Midford (NESCent)
Start Date: 15-Sep-2009
End Date: 15-Dec-2009
Keywords: phylogenetics, comparative methods

Ontologies are becoming increasingly popular as a way to capture biological knowledge. Ontologies are collections of terms and a small set of relations that can apply between these terms. Recently, ontologies have been developed that can be used to describe observable characteristics of organisms in large taxonomic groups (e.g., fish, amphibians, hymenopteran insects). However, when ontologies are used to describe more than one species, a term applied to one species may or may not have the same meaning when applied to another species. Furthermore, there are different ways for biological terms to have the same meaning. Homology, or similarity due to descent from a common ancestor, is arguably the most important in evolutionary biology, but different kinds of observable evidence, such as similarity in structure, function, anatomical location or development can be used to infer other evolutionary processes, such as convergence, in the absence of homology. This project will extend existing methods of matching terms across ontologies to incorporate phylogenetic information in the matching process and to construct different types of matches. A proof-of-concept prototype will be developed and used as a component of an open-source comparative methods tool.