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Knowledge Representation & Applications
(Mostly Biomedical applications)

MEBI 550, Winter, '05

Assignment Calendar:

Week of Topic Reading assignments Written assignments
Jan 4 Intro Thu: Ontology 101 (Noy, '01)  
Jan 11 KR in biology Tue: What is a KR? (Davis etal, '93)
Thu: Ontology for Bio Function (Karp. '00)
Exercise 1: Ontology building (Wed)
Jan 18 KR in DSS Tue: Mycin (Davis etal, '77) & Arden (Hripsak etal, '94)
Thurs: Guidelines (Wang etal, '02)
Reaction paper #1 (on the Mycin paper, due Tue)
Jan 25 KR in anatomy

Tue: the FMA (Rosse & Mejino '03; Smith & Rosse '04)
Thurs: Grail and Galen (Rector et al '97)

Final Project checkpoint #1 (Tue)
Feb 1 Inference & Tractability Thurs: Brachman & Levesque, '87

Exercise 2: Ontologies and rules (Tue)

Feb 8 Theorem proving Tue: Knowledge Sharing (Neches etal '91) and the OKBC paper (Chaudhri etal '98)

Exercise 3: Logic & theorem-proving (Tue)
Final Project checkpoint #2 (Wed, 9am)
Logic & theorem-proving exam (Thurs)

Feb 15 Gene Ontology Tues: RiboWeb paper, GO paper (2001)
Thurs: DLs and GO (Wroe), Oil & Bioinformatics (Stevens)
Reaction paper #2 (On the Stevens "OIL" paper, due Thurs)
Feb 22 Semantic Web and OWL Tues: TimBernersLee (2001), Hendler's Agents (2001);
Thurs: UMLS as a DL (Hahn+Schulz)
Final Project checkpoint #3 (Thurs)
March 1 DBs, Prolog & Deductive DBs Tues: No reading;
Thurs: Richardson's collaborative KBs ('03)
Exercise 4: OWL hands-on (Tues)
March 8 Cyc
(& final review)
Tues: Guha & Lenat (1994) 3-4 Final project presentations (Thurs)
March 16 Finals week exam block: 3/16, 10:30am - 12:30pm Final projects due (Wed); 6-8 presentations.

All reading assignments can be retrieved from the course Eres pages.

General expectations:

Assignments fall into three categories: (1) Reaction essays that aim to improve your ability to read critically and write clearly, (2) Hands-on exercises that will help understand the nuts-and-bolts of knowledge representation issues, and (3) the Final project, that will allow you to pursue one area in much greater detail.

I expect all assignments to be completed on-time (at the start of class session, unless otherwise noted). Typically, I will plan on discussing these assignments in class. Therefore, late assignments will be significantly down-graded.

Reading assignments: Generally speaking, the selected readings are from the primary literature -- one objective for the course is to hone your ability at reading and critiquing such papers. As indicated above, you must critically read and respond to two of the reading assignments in your written reaction essays.

Exercises: All assignment specifications are now available: Exercise #1, "building an Ontology"; Exercise #2, "building and using an ontology"; Exercise #3, on theorem proving; and Exercise #4, "building an OWL ontology".

Final projects : Project specification information is now available.

Last Updated:
Feb 23, '05

Contact the instructor at: gennari@u.washington.edu