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

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.

• 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 the Ontology of Physics for Biology (the OPB, authored by Dan Cook). There are several thrusts of the SPB group:
  • In collaboration with the Virtual Physiological Rat project, we aim to demonstrate how our approach and a library of biosimulation models can accelerate research.
  • We developed SBOL (together with many others) as a standard for specifying parts and reusable libraries for synthetic biology.
  • We collaborated 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 Herb Sauro and others, we are building a Center for Reproducible Biological Models.

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Teaching:

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!):

• Ph.D. graduates: Chunhua Weng, Ching-Ping Lin, Maxwell Neal, Michal Galdzicki, Wynona Black, Alan Kalet, Rebecca Hazen, Nikhil Gopal, Graham Kim, Lucy Wang, Ahmad Aljadaan
• Ph.D. students: Ryan James, Harkirat Sohi

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 almost 30 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.

• Wang LL, Hayman T, Smith JR, Tutaj M, Shimoyama ME, Gennari JH (2019). Predicting instances of Pathway Ontology classes for pathway integration. Journal of Biomedical Semantics
• Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, and Gennari JH (2018). SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty829
• Neal, ML, Carlson, BE, Thompson, CT, James RC, Kim KG, Tran T, Crampin EJ, Cook DL, & Gennari JH (2015). Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PLoS ONE doi: 10.1371/journal.pone.0145621.
• Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH (2014). A reappraisal of how to build modular, reusable models of biological systems. PLoS Computational Biology.
• Galdzicki, M., a host of SBOL-Developers, Gennari JH, Myers CJ, and Sauro, HM (2014). SBOL: A community standard for communicating designs in synthetic biology. Nature Biotechnology 32(6): pp. 545-550.
• Cook, DL, Neal, ML, Bookstein, FL, and Gennari, JH (2013). Ontology of Physics for Biology: representing physical dependencies as a basis for biological processes, Journal of Biomedical Semantics.
• 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.10.1371/journal.pone.0017005
• 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.
• 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 .
• 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.
• 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.

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