Representing Phenotypes in OWL

In simple terms, a phenotype is a collection of characteristics that arise through the expression of the genes of an organism, in an environment. Some examples of phenotypes are the red eyes of a typical fruitfly, Drosophila melanogaster; the length of a body part such as the tail of a mouse; high blood pressure in the arteries of a human, sensitivity to a chemical or to light; reduced mass of an organ or part of an organism such as bone. In biology, we are often interested in how variations in genotype and environment can lead to variations in phenotype. There is a wealth of research to draw from, but much of the knowledge is currently encoded in natural language and free text in the literature and biological databases[?] if this knowledge can be captured using ontologies and ontological formalisms we increase the range of computational methods that can be used to analyse this data[?]. This paper describes the OWL translation of a formalism for representing phenotypes making use of the ontologies that comprise Open Bio-Ontologies Foundry (http://www.obofoundry.org). Many of these ontologies such as the Gene Ontology[?], the Foundational Model of Anatomy[?] and the Cell Ontology[?] represent canonical biology, which is to say the biology of “normal”, “typical” or healthy organisms. We use these ontologies as building blocks that can be combined with an ontology of qualities to construct descriptions of phenotypes, many of which deviate from canonical biology. This methodology can be used in a variety of different kinds of investigations. The reader of this paper should be aware that the end-user of the software systems and databases built around the formalism presented do not work directly at level of OWL constructs, or at their OBO-Formalism equivalents. They typically interact via intermediate representations and user interfaces such as Phenote more details can be found on the phenotype ontology website. We present the OWL version of the formalism in order to give it a grounding in logic, and as a means of leveraging OWL-based tools and reasoning engines, although space dictates we do not discuss these applications.