Towards Improving Phenotype Representation in OWL

Abstract

Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize hu- man diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected en- tities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. We analyze the OWL-based formalizations of complex phenotype descriptions based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. In particular, we suggest a novel, role-based approach to represent relational qualities such as Con- centration of calcium in blood, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. Our analysis of OWL-based representation of pheno- types can contribute to improving consistency and expressiveness of formal phenotype descriptions.