MEBI 550: Knowledge Representation and Applications
J. Kalet, Ph.D.
Professor, Radiation Oncology
Professor, Medical Education and Biomedical Informatics
Adjunct Professor, Computer Science and Engineering,
and Biological Structure
Office: NN146A University of Washington Medical Center
Telephone: (206) 598-4107
MEBI 550 deals with the principles of knowledge representation and
reasoning, with application to biology, medicine and health. Many of
the examples will use the Common Lisp programming language, but prior
knowledge of Lisp is not assumed. Other programming and knowledge
representation languages will also be introduced, such as Prolog.
Grading and other policies
The course assumes previous programming experience at the level of UW
CSE 142 Computer Programming I. However, it is not important which
programming language you know, as long as you are experienced with at
least one. In addition, the course requires certain basic computing
skills and mathematical background. These are listed on the Prerequisites page.
Course learning objectives
A list of course learning objectives
illustrates what students can expect to be able to know and do by
the end of the course.
Web resources on biomedical informatics projects
- The UW Structural
Informatics Group has a project, the Foundational Model of
Anatomy, that captures knowledge about human anatomy in a rich
- The Pacific Symposium on
Biocomputing is an annual conference with a published proceedings
of high quality papers.
- The Unified
Medical Language System is a very large lexicon of medical terms
and relationships between them.
- The PharmGKB project is
building an ontology for drugs and genetic variations related to drug
responses in individuals.
- The Center for Computational
Pharmacology at the University of Colorado has a range of
interesting projects modeling biomolecular pathways and analysing
gene expression data.
- The Children's Hospital
Informatics Program at Harvard has developed software for a
variety of bioinformatics projects.
- BioCyc is a collection of
Pathway/Genome knowledge resources that each provides a description of
the genome and metabolic pathways of an organism. At present 160
organisms are covered.
- The Pathway Tools
Information Site has information on how to use the Pathway Tools
software with the BioCyc databases. There is a link on this page to
for using the Lisp API.
- The Gene Ontology
project, which has constructed a hierarchical classification system
representing knowledge about gene products according to molecular process,
cellular function and cellular component.
Web resources on Lisp
Some links for more information on Common Lisp and related topics are
on the Common Lisp information page
Other Web resources
Information from specific quarters
Information from specific years in which I taught the course is at the