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
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, 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.
- 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.
- In collaboration with Herb Sauro, we are carrying out work to standardize parts and create a parts library for synthetic biology. Along the way, we developed SBOL (together with many others).
- 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.
- With Professor Mark Phillips of Radiation Oncology, I co-lead an "Informatics in Radiation Oncology and Knowledge representation" (IROK) research group. We are currently exploring two (very) different research directions. One is to apply Bayes Nets to assess the quality of radiation treatment plans, based on prior knowledge of "good" plans, and then to explore an "Ontology" approach to construction of such Bayes' nets. The other direction is to elicit patient symptoms to better track progression and enable quality follow-up decisions after radiation treatment for brain cancers and brain metastases.
- With Neil Abernethy, I am exploring network analysis of large bio-informatics resources, notably microarray gene expression results, pathway knowledge bases, and protein-protein interaction networks.
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, '13:Honors 222C: Transformational technologies for biology, medicine & health
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
- Ph.D. students: Rebecca Hazen, Nikhil Gopal, Graham Kim, Ahmad Aljadaan, Lucy Wang, Ryan James
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 more than 20 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.
- 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.
- 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.
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 Nov, 2016
Photo: Eastsound, on Orcas Isand. July, 2012