Enabling Ontology Based Semantic Queries in Biomedical Database Systems.

Abstract

While current biomedical ontology repositories offer primitive query capabilities, it is difficult or cumbersome to support ontology based semantic queries directly in semantically annotated biomedical databases. The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems. To fully realize semantic query capabilities based on ontologies, we develop a system DBOntoLink to provide unified semantic query interfaces by extending database query languages. With DBOntoLink, semantic queries can be directly and naturally specified as extended functions of the database query languages without any programming needed. DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal. We demonstrate the use of DBOntoLink in a real world biomedical database with semantically annotated medical image annotations.