There is a lack of tools to ease the integration and ontology based semantic queries in biomedical databases, which are often annotated with ontology concepts. We aim to provide a middle layer between ontology repositories and semantically annotated databases to support semantic queries directly in the databases with expressive standard database query languages. We have developed a semantic query engine that provides semantic reasoning and query processing, and translates the queries into ontology repository operations on NCBO BioPortal. Semantic operators are implemented in the database as user defined functions extended to the database engine, thus semantic queries can be directly specified in standard database query languages such as SQL and XQuery. The system provides caching management to boosts query performance. The system is highly adaptable to support different ontologies through easy customizations. We have implemented the system DBOntoLink as an open source software, which supports major ontologies hosted at BioPortal. DBOntoLink supports a set of common ontology based semantic operations and have them fully integrated with a database management system IBM DB2. The system has been deployed and evaluated with an existing biomedical database for managing and querying image annotations and markups (AIM). Our performance study demonstrates the high expressiveness of semantic queries and the high efficiency of the queries.
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