John Gennari
Associate Professor
Biomedical & Health Informatics
University of Washington



Telephone: (206) 616-6641
Complete contact information



Research Goal:

My goal is to help build good knowledge-based systems that support knowledge sharing
for applications in Biomedical & Health Informatics

(One might ask :What is Biomedical & Health Informatics? )

My research focus has been to support knowledge sharing. I use this term broadly, and associated research questions cover issues such as knowledge representation, ontology alignment, and interoperation of on-line resources, and even human-human communication in support of knowledge sharing. I have research interests in areas such as:

Matching these research interests, I regularly attend AMIA, the annual American Medical Informatics Association symposium, and ICBO, the International Conference on Biomedical Ontologies. I also have attended the Pacific Symposium on Biocomputing, and K-Cap, the Knowledge Capture Conferences.

Research Projects:

My current research focuses on knowledge based systems that help with knowledge sharing. This broad goal can be applied in a variety of ways to a variety of BHI domains. Here is a list of current projects; for past projects, see my publication list.


Here are my most recent syllabi and course information for Biomedical and Health Informatics (BHI):

Fall, '14: BIME 530: Introduction to Biomedical and Health Informatics
Winter, '15:
MEBI 550: Knowledge representation and biomedical applications
Spring, '18: BIME 498: Transformational technologies for biology, medicine & health (an undergraduate course)

I hold some strong opinions about what makes a good oral presentation--and I have a teaching presentation about how to avoid common problems and pitfalls when giving a scientific oral presentation.

Mentoring (an important subclass of teaching!):


I've been a student, and received diplomas from  Colgate University, University of Wisconsin - Madison, and at the University of CA - Irvine. My Ph.D. from UC-Irvine (1990) was in the area of machine learning. Strangely enough, I returned to UW-Madison as a visiting assistant professor for one year ('91-'92), and to UC-Irvine as an adjunct assistant professor for three years ('98-'01). In between, I received my biomedical informatics training by being a research scientist at Stanford Medical Informatics, where I helped develop the Protégé system.

I also spent one year teaching Computer Science at Keio University in Japan. It was almost 30 yrs ago, but ask me about it; I still love to talk about Nihon.


Below is a list of my current favorite (recent or best) publications.

Contact Information:

I am an Associate Professor in the Division of Biomedical & Health Informatics, in the Department of Biomedical Informatics and Medical Education , in the School of Medicine, University of Washington. (Whew!)

Mailing address:

John Gennari
Dep't of Biomedical Informatics and Medical Education
University of Washington
850 Republican St., Bldg C
Seattle, WA 98019-4714

Office location: rm 483, Building C, South Lake Union UW Medicine Research Center

Campus mail: Box 358047

Fax: 206-221-2671

Obviously, the best way to contact me is via email, and secondarily via my office phone (616-6641).

Last updated April, 2019
Photo: Eastsound, on Orcas Isand. July, 2012