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
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:
- 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.
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!):
- 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
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
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.
- 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.
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!)
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
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