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Open Access Highly Accessed Methodology article

Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies

Robert Hoehndorf123*, Frank Loebe23, Janet Kelso1 and Heinrich Herre23

Author Affiliations

1 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany

2 Institute of Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany

3 Institute for Informatics, University of Leipzig, Johannisgasse 26, 04103 Leipzig, Germany

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BMC Bioinformatics 2007, 8:377  doi:10.1186/1471-2105-8-377

Published: 9 October 2007

Abstract

Background

Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. However, semantic extensions are required to meet the OBO Foundry interoperability goals. Inconsistencies may arise when ontologies of properties – mostly phenotype ontologies – are combined with ontologies taking a canonical view of a domain – such as many anatomical ontologies. Currently, there is no support for a correct and consistent integration of such ontologies.

Results

We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. This is achieved by adding an extension to the semantics for relationships in the biomedical ontologies that allows for treating canonical information as default. Conclusions drawn from default knowledge may be revoked when additional information becomes available. We show how this extension can be used to achieve interoperability between ontologies, and further allows for the inclusion of more knowledge within them. We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach.

Conclusion

Biomedical ontologies require a new class of relations that can be used in conjunction with default knowledge, thereby extending those currently in use. The inclusion of default knowledge is necessary in order to ensure interoperability between ontologies.