Knowledge Representation and Biomedical Applications
MEBI 550, Fall 2012
Assignment Calendar: (will be updated throughout the quarter)
| Week of | Topic | Reading assignments | Homeworks, exams |
| Sept 24 | Intro & Motivation | BernersLee 2001 (Wed) Allemang & Hendler text - chpt 3: RDF (Wed) |
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| Oct 1 | What are the data? Sharing data... Querying data |
Text, chpt 5 portion: Thru p. 88 only (Mon) |
Project #1 due Wed |
| Oct 8 | More querying |
Karp: Pathway Databases, 2001 (Mon) |
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| Oct 15 | Inference, logics, |
Chptr 2 from Thinking on the Web (Mon) |
Project #2 due Wed |
| Oct 22 | RDFS, Rule-based systems, and Tractability | Davis, Buchanan & Shortliffe: MYCIN (1977) (pp. 15-25 only) and |
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| Oct 29 | Resolution & Theorem proving -- intro to OWL & Description logic | Allemang & Hendler text - excerpts from chpts 8, 11 (Mon). |
Resolution exercise due Mon |
| Nov 5 | One-on-one meetings | No readings due (AMIA) |
see Matt Horridge's OWL tutorial for Protege4 (15 Meg!) |
| Nov 12 | OWL and Open World |
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Project #3 individual part due Tues Project #3 group part due Friday, 11/16 |
| Nov 19 | Probability & Bayes nets | Henrion et al, 1991: Decision Analysis (Monday) You should also read the straightforward tutorial on Bayes Net, provided by the developers of "Netica" |
Project #4 check point #1 due Wed |
| Nov 26 | Rules and the Sem Web | Gooch, 2011: Review of challenges for process-oriented HIS. (Monday) |
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| Dec 3 | Temporal KR and review | O'connor, et al. 2009: Temporal Reasoning for clinical trials (Mon) . | Project #4 due Friday, Dec 7th |
| Mon, Dec 10 | Final presentations | Oral presentations |
The required textbook for this class is The Semantic Web for the Working Ontologist, (second edition) by Allemang and Hendler, 2011. Available from Amazon.
All reading assignments can be retrieved from the course Eres pages.
General expectations:
My general expectation is that we (both the students and myself) will learn over a whole bunch about knowledge representation and ontologies, and how they can be applied to biomedical applications. I will teach this course as an interactive seminar; as it is a small group, there will be plenty of opportunity for participation by all.
I expect you to be adult learners. I am assuming you want to be in class, and that you want to learn the material I'm advertising to teach. I will therefore also expect to learn from you -- teaching and learning work best when it is a two-way street. I will do my best to listen, and not just lecture!
Reading assignments:
In addition to (obviously) reading these prior to class, I also expect you to be able to discuss them in class. (E.g., I may start class by simply asking you "So, whaddya think of the reading?") In some cases, this may require multiple readings; it certainly means that you must think about what you read, and probably taking notes to help you offer discussion points and ideas during class. To help with this task, I am requiring you to write and post at least a couple of paragraphs about each assigned reading to the class message board (Catalyst GoPost).
Thus, for each reading assignment listed above, please tell me (and your peers) something new that you learned from the reading, or some personal reaction, and perhaps some questions. Your postings can certainly be informal (a carefully organized essay is not expected). You should certainly read other students' posts, and you may also reply or respond to these postings. In some cases, I may jump in with my own comments or reactions. A goal of this message board is to generate discussion and questions even prior to class. Please post by noon of the day the assignment is due, so that I can read them before class. .
Projects:
There are four projects, and each is described in a separate web page: see above. Projects are to be handed in electronically, via the course catalyst drop box.
Last Updated:
Nov, '11
Contact the instructor at: gennari@uw.edu