Instructor: John Gennari, 616-6641
Class location/times: Health Sciences T663; Mon/Wed, 1pm -- 2:20pm
Office hours: By appointment

Course description:

What is a knowledge representation? Why are choices in knowledge representation important for biomedical informatics application builders? How does one manipulate and store knowledge and data so that it can be queried and used by systems and services in an intelligent manner? How do I build an ontology? How are ontologies and knowledge representations used in the Semantic Web? How is knowledge shared?

These are some of the questions we pursue in this course. To address these questions, we begin by investigating what biomedical data are, both in clinical and in bioinformatics settings. This is a graduate-level, research-focused course, with readings both from the primary literature as well as selected chapters from a semantic web textbook. A goal is to explore some of the foundational, theoretical choices in KR, and to understand how these affect current biomedical informatics applications.

Week-by-week course summary and assignments

Course objectives:

Distinguish among knowledge representational formalisms, and provide examples in biomedical domains. These formalisms range from OO systems to rule-based systems to description logics.
Understand the implications and potentials of semantic web representations (XML, RDFS, and OWL) and technologies
Carry out semantic web queries -- e.g., via SPARQL
Distinguish between explicit knowledge and inferred knowledge
Describe the implication of formal results around tractabilty and decidability for inference systems
Build simple ontologies for applications in biomedical informatics

Required textbook:

Semantic Web for the Working Ontologist, (second edition) by Allemang and Hendler, 2011.
Available from Amazon.

Expectations:

I expect you to be 21st century citizens: to be responsive to email, and to read the relevant web pages. In turn, I will be responsive to any question or concerns you may have.

I expect you to all be adult learners, and that your goal is to learn something about BHI. You should be prepared to learn from your peers as well as from me. In turn, I am prepared to learn from you. Learning from peers (and students) requires an ability to listen, a willingness to speak, and a respect for all participants.

I expect you to know and understand academic honesty. To prevent misunderstandings, I expect all students to read The University of Washington's statement on Student Academic Responsibility. All students are expected to follow high standards of academic honesty in all aspects of this course.

Religious accommodations

Washington state law requires that UW have a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy. Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form.

BIME 550 A Wi 20: Knowledge Representation And Applications