Research Goal:

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

However, this leads to two questions:

• Knowledge reuse, mappings, and alignments among differing models (or ontologies)
• Knowledge representation for anatomy (see FMA), physiology, and cell-signaling pathways
• Knowledge representation and tools for clinical trial protocols and health-care guidelines

Matching these research interests, there are at least two conferences I attend regularly: AMIA, the annual American Medical Informatics Association symposium, and K-Cap, the Knowledge Capture Conferences, held every other year. (I was co-chair of K-Cap '03, and am workshop chair for K-Cap '07.)

• Together with Dan Cook, I co-lead a “Semantic Simulation” research group that studies how improved semantics (via good ontology building) can improve bio-simulation models. In particular, we are trying support the construction of re-usable libraries of bio-simulation models. We take as inspiration the model of a Physiome, where researchers build multi-scale, multi-domain models that capture the complexity of physiology and pathology. This research leverages both the Foundational Model of Anatomy, (FMA)and an Ontology of Physics for Biologists (the OPB, authored by Dan Cook). This work is part of a broader collaboration with Jim Brinkley and the National Center for Biomedical Ontology at Stanford.
• In collaboration with the Structual Informatics Group within BHI, I am working with the Foundational Model of Anatomy(FMA), a VERY large knowledge base of human anatomy (built using the Protégé system). Because anatomy is central to much of biology, the FMA can be used to connect to other biomedical ontologies. For example, physiology is not in the FMA, yet clearly relates to anatomy. Likewise, the Gene Ontology contains information about gene products, yet ultimately these genes operate within the anatomy of a cell. More specifically, I am leading efforts to do ontology alignment where two ontologies (e.g. the Gene Ontology and the FMA) are connected without actually merging them. For more information please see my ontology alignment web page.
• In collaboration with Jesse Wiley and Dan Cook, I am looking at knowledge modeling for cell-signaling pathways. More specifically, we are looking at pathways that may be relevent to the pathogenesis of Alzheimer's disease.
• With my student Ping Lin and with Tom Payne, we studied the effectiveness of alerting systems within the Puget Sound's VA's CPOE system. Partially inspired by our experience there, Ping is carrying out observational studies of the ordering process (including CPOE) at Children's Hospital, and will be applying Cognitive Work Analaysis for her dissertation research in this arena. Ultimately, we hope this work we lead to a better understanding of ordering workflow and to ideas for how to re-design the entire process.

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Teaching:

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

Spring, '08: MEBI "498": Transformational technologies for biology, medicine & health
Spring '08: MEBI 591: Biosimulation & Semantics seminar
Fall, '07: MEBI 537: BHI Research Methods
Fall, '06: MEBI 538: BHI Research Methods
Winter, '05: MEBI 550: Knowledge representation and (biomedical) applications
Fall, '04: MEDED 530: Introduction to biomedical & health informatics

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. One type of presentation common for learning about research in BHI is a "Journal Club" presentation. Wanda Pratt has a good presentation specifically on how to do a journal club presentation.

I also taught an odd database course in Fall of '02 called "Databases and applications in the health sciences". At my previous job (UC, Irvine) I taught "Introduction to Artificial Intelligence" (see old web pages for graduate level version and undergraduate version).

Mentoring (an important subclass of teaching!):

• Ph.D. graduate: Chunhua Weng
• Ph.D. students: Michal Galdzicki, Ching-Ping Lin, Maxwell Neal

Background:

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 all of my medical 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. Ask me about it.

Publications:

Below is a list of my current favorite (recent or best) publications. Abstracts or full-text PDFs are available for most of these.

• Gennari, J.H., Neal, M.L., Carlson, B. and Cook, D.L. (2008). Integration Of Multi-Scale Biosimulation Models Via Light-Weight Semantics. Proceedings of the Pacific Symposium on Biocomputing, 2008, pp. 414 – 425 .
• Cook, D.L, Wiley, J.C., and Gennari, J.H. (2007). Chalkboard: Ontology-based pathway modeling and qualitative inference of disease mechanisms. Proceedings of the Pacific Symposium on Biocomputing 2007, pp. 16-27 .
• Au, A., Li, X., and Gennari, J.H. (2006). Differences Among Cell-structure Ontologies: FMA, GO, & CCO. Proceedings of the AMIA Annual Fall Symposium, pp. 16-20, Washington DC.
• Li, H., Gennari, J.H., and Brinkley, J.F. (2006). Model Driven Laboratory Information Management Systems. Proceedings of the AMIA Annual Fall Symposium, pp. 484-488, Washington DC.
• Travillian, R.S., Gennari, J.H., and Shapiro, L.G. (2005) Of Mice and Men: Design of a comparative anatomy information system. Proceedings of the AMIA Annual Fall Symposium pp. 735-739, Washington DC.
• Gennari, J.H., Weng, C., Benedetti, J. and McDonald, D.W. (2005) Asynchronous communication among clinical researchers: A study for systems design. International Journal of Medical Informatics, 74(10), 797-807.
• Gennari, J.H., Silberfein, A., and Wiley, J.C. (2005). Integrating genomic knowledge sources through an anatomy ontology. Proceedings of the Pacific Symposium on Biocomputing 2005, pp. 115 - 126.
• Weng, C., and Gennari, J.H. (2004). Asynchronous collaborative writing through annotations, Proceedings of the ACM Conference on Computer Supported Cooperative Work (CSCW'04), pp. 578–581, Chicago.
• Pratt, W., Reddy, M.C., McDonald, D.W., Tarczy-Hornoch P., and Gennari, J.H. (2004). Incorporating Ideas from Computer-Supported Cooperative Work. Journal of Biomedical Informatics, 37, 128-137.
• Weng, C., McDonald, D.W., and Gennari, J.H. (2004). A collaborative clinical trial protocol writing system. Proceedings of MedInfo 2004, San Francisco, CA. pp. 1481-1485.
• J.H. Gennari, M.A. Musen, R. Fergerson, & a bunch of other Protégé geeks. (2003) The Evolution of Protégé: An environment for knowledge-based systems development. International Journal of Human-Computer Studies, vol 58 (1): 89-123.
• J. H. Gennari, D. Sklar, & J. Silva, (2001). Cross-tool communication: From protocol authoring to eligibility determination. Proceedings of the AMIA Annual Fall Symposium, pp. 199-203. Washington, DC.
• L. Ohno-Machado, J.H. Gennari & a cast of thousands.(1998) The GuideLine Interchange Format: A Model for Sharing Guidelines. Journal of the American Medical Informatics Association, 5(4), pp. 357-372.
• J. H. Gennari, R. B. Altman, & M.A Musen. (1995) Reuse with Protégé-II: From Elevators to Ribosomes. Proceedings of the Symposium on Software Reuse, pp. 72-80. Seattle, WA.
• J. H. Gennari, S. W. Tu, T. E. Rothenfluh and M. A. Musen.(1994) Mapping Domains to Methods in Support of Reuse. International Journal of Human-Computer Studies, 41, 399-424.

Contact Information:

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

Mailing address:

John Gennari
Dep't of Medical Education and Biomedical Informatics
University of Washington
1959 NE Pacific Street, Box 357240
Seattle, WA 98195-7240

Office location: I-264C Health Sciences Center

Fax: 206-543-3461

Obviously, the best way to contact me is via email, and secondarily via my office phone (616-6641). I do not recommend trying to find the room I-264C unless you are a frequent visitor to the Health Sciences Center, and even then, it could be a challenge...

Last updated April, 2008
Photo: That's my own backyard, after a rare March '08 snowfall (yes, those are real snowmen with real green grass)