Email updates

Keep up to date with the latest news and content from Journal of Biomedical Semantics and BioMed Central.

This article is part of the supplement: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011)

Open Access Open Badges Proceedings

Towards improving phenotype representation in OWL

Frank Loebe1*, Frank Stumpf1, Robert Hoehndorf2 and Heinrich Herre3

Author Affiliations

1 Department of Computer Science, University of Leipzig, 04103 Leipzig, Germany

2 Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK

3 Institute of Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, 04107 Leipzig, Germany

For all author emails, please log on.

Journal of Biomedical Semantics 2012, 3(Suppl 2):S5  doi:10.1186/2041-1480-3-S2-S5

Published: 21 September 2012



Phenotype 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.


We 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.


In 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.


Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions.