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

Hoehndorf

BMC Bioinformatics (2007) PMID 17925014 PMCID 2180186

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.

DOI: 10.1186/1471-2105-8-377
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