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? )

• Knowledge reuse, mappings, and alignments among differing models (or ontologies)
• Ontology building, and use of semantic web methods for effective use of knowledge bases
• Knowledge representation and knowledge sharing for Synthetic Biology (see SBOL).
• Knowledge representation for anatomy (see FMA), physiology (see OPB), and cell-signaling pathways
• Knowledge representation and tools for clinical trial protocols and health-care guidelines

Matching these research interests, I regularly attend AMIA, the annual American Medical Informatics Association symposium. I also have attended the Pacific Symposium on Biocomputing, and K-Cap, the Knowledge Capture Conferences. (I was co-chair of K-Cap '03.)

• Together with Dan Cook, I co-lead a Semantics for Biological Processes 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. This research leverages both the Foundational Model of Anatomy, (FMA)and an Ontology of Physics for Biology (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. There are two thrusts of the SPB group:
  • In collaboration with Herb Sauro, and Clark & Parsia, LLC, we are carrying out work to standardize parts and create a parts library for synthetic biology.
  • As part of the Ricordo project, we are collaborating with the European Virtual Physiological Human project to work towared the Physiome vision, where researchers build multi-scale, multi-domain models that capture the complexity of physiology and pathology.
• 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. I am interested in 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.
• Working with Wynona Black, we are applying data mining methods to a very large, longitudinal database of EMR records of patients with Acute Coronary Syndrome (aka heart attack patients). The idea is to look at actual patterns of care (including temporal patterns) versus healthcare guideline recommendations.
• Together with Nick Anderson, I recently completed work on Cross-Institutional Clinical Translational Research (CICTR; this project is part of the ITHS Biomedical Informatics Core). Our goal was to build systems that allow for cross-institutional clinical research queries, such as queries in support of clinical trial protocols. To enable such queries, clinical terms must be linked to each other, even if they may use different terminology standards.

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Teaching:

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

Spring, '13: Honors 222C: Transformational technologies for biology, medicine & health
Fall, '12: MEBI 550: Knowledge representation and biomedical applications
Fall, '09: MEBI 537: BHI Research Methods
Winter, '05: MEBI 550: Knowledge representation and (biomedical) applications

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. graduates: Chunhua Weng, Ching-Ping Lin, Maxwell Neal, Michal Galdzicki
• Ph.D. students: Wynona Black. Alan Kalet
• Currrent postdocs: Maxwell Neal, Michal Galdzicki

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 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 more than 20 yrs ago, but ask me about it; I still love to talk about Nihon.

Publications:

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

• Neal, M.L., Cook, D.L. and Gennari, JH (2013). An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome. Proceedings of the International Conference on Biomedical Ontology.
• Cook, D.L., Neal, ML, Hoehndorf, R, Gkoutos, GV, and Gennari, JH. (2013). Representing physiological processes and their participants with PhysioMaps, Journal of Biomedical Semantics.
• Cook, D.L., Bookstein, F.L., Gennari, J.H. Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology. PLoS ONE, 2011. 6(12): e28708
• Cook, DL, Galdzicki, M, Neal, ML, Mejino, JLV, and Gennari, JH (2011). HeartCyc, a cardiac cycle process ontology based in the Ontology of Physics for Biology. Proceedings of the International Conference on Biomedical Ontology.
• Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H.M., and Gennari, J.H. (2011) Standard Biological Parts Knowledgebase. PLoS ONE.
• Ching-Ping Lin and John H. Gennari (2011). Understanding the Work of Pediatric Inpatient Medicine Teams: Implications for Information System Requirements. Proceedings of the AMIA Annual Symposium, Washington, DC.
• Gennari, JH, Neal, ML, Galdzicki, M, Cook, DL. (2011) Multiple Ontologies in Action: Composite Annotations for Biosimulation Models. Journal of Biomedical Informatics, pp. 146-154.
• Neal ML, Gennari JH, Arts T, Cook DL (2009). Advances in semantic representation for multiscale biosimulation: A case study in merging models.” Pacific Symposium on Biocomputing, pp. 305-315, 2009.
• Lin, C., Payne, TH, Nichol, WP, Hoey, PJ, Anderson, CL, and Gennari, J.H. (2008). Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates. Journal of the American Medical Informatics Association, 15(5), 620-626.
• 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.
• 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., 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.

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
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 Jan, 2013
Photo: Eastsound, on Orcas Isand. July, 2012