John Gennari, PhD

Associate Professor, Biomedical Informatics and Medical Education



Ontologies, knowledge sharing, semantic web,


PhD (Computer Science) UC-Irvine. Experience: Protege developer at Stanford Medical Informatics.

Current research:

Primary focus on semantic web, knowledge representation and ontology development.  See web pages for other interests: synthetic biology, physics-based biosimulation, health-care guidelines / protocols, and cellular signaling pathways.


Currently accepting new students.

Representative publications:

  • Galdzicki M, Rodriguez C, Chandran C, Sauro HM, Gennari JH. (2001). Standard Biological Parts Knowledgebase. PLoS ONE 6(2):e17005.
  • Gennari JH, Neal ML, Galdzicki M, and Cook DL. (2011). Multiple Ontologies in Action: Composite Annotations for Biosimulation Models. Journal of Biomedical Informatics 44(1):146-154.
  • Gennari JH, Neal ML, Carlson B, Cook DL. (2008). Integration of Multi-Scale Biosimulation Models Via Light-Weight Semantics. Proceedings of the Pacific Symposium on Biocomputing, pp. 414-425, 2008.
  • Weng C, McDonald DW, Sparks D, McCoy J, and Gennari JH (2007). Participatory design of a colloborative clinical trial protocol writing system. The International Journal of Medical Informatics 76(S1), 245-251.
  • Gennari JH, Musen MA, Fergerson RW, Grosso WE, Cruzbezy M, Eriksson H, Noy NF, and Tu SW (2003). The Evoluation of Protege: An Environment for Knowledge-Based Systems Development. International Journal of Human-Computer Studies, 58, 89-123.