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

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 b...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Robert Hoehndorf, Frank Loebe, Janet Kelso, Heinrich Herre
• Keywords: Biomedical Ontologies, BMCBI 2007, Interoperability, Ontologies