Abstract
BackgroundPhenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies.MethodsWe analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges.ResultsIn particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, 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.ConclusionOur analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions.
Highlights
In recent years, molecular biology has made significant progress in understanding the mechanisms underlying human disease
To standardize the terminology used in describing phenotypes, multiple speciesspecific phenotype ontologies were developed
Identification of basic problems We see three basic problems that need to be addressed regarding the representation of phenotypes and the interpretation of EQ descriptions in terms of the Web Ontology Language (OWL) [24], in order to utilize automated and semantically correct reasoning to its full extent
Summary
Molecular biology has made significant progress in understanding the mechanisms underlying human disease. Several studies investigate disease mechanisms in animals that serve as models for humans [1]. The targeted modification of the genetic markup of these organisms provides a powerful means to investigate the molecular mechanisms associated with heritable diseases in humans [2]. The observable characteristics of these modified organisms (their phenotypes) are represented in model organism databases and can be utilized to suggest candidate genes for diseases for which no molecular origin is currently known [3]. The Human Phenotype Ontology (HPO) [7] describes phenotypes in humans and is applied for describing human diseases and individual patients. Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies
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