He is interested in applying knowledge representation and reasoning, natural language processing and semantic web techniques to biomedical informatics research. In current, he investigates methods and tools to facilitate the discovery, analysis, and integration of heterogeneous, evolving biomedical datasets originating from multiple sources.

He was involved in the development of Protégé, WebProtégé and CEDAR—tools for building ontologies and for creating and semantically annotating metadata. He has also taught courses on ontology engineering, knowledge representation and reasoning, and software development.