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Knowledge Representation and Biomedical Applications
MEBI 550, Fall 2013

Assignment Calendar: (will be updated throughout the quarter)

Week of Topic Reading assignments Homeworks, exams
Sept 23 Intro & Motivation BernersLee 2001 (Wed)
Sept 30 What are the data?
Sharing data...
Querying data

Allemang & Hendler text - chpt 3: RDF (Wed)
Bio2RDF: Belleau, 2008 (Wed)
Text, chpt 5 portion: Thru p. 88 only (Wed)

Oct 7

More querying
Classes and Ontologies

Ontology Development 101, thru the end of section 3 (Mon)
Karp: Pathway Databases, 2001
Wed: No reading due

Project #1 due Wed
Oct 14

Inference, logics,
Frames, Rules

Demir et al, 2010 (Mon)
Davis, Schrobe, & Szolovitz, 1993 (Mon)
Chptr 2 from Thinking on the Web
Text, chpt 6 (Wed)

Oct 21 RDFS, Rule-based systems, and Tractability

Text, portion of chpt 7, thru pp. 133 -- stop at "Modeling combinations and patterns", and pp. 142--146, about domain and range. (Mon)
Davis, Buchanan & Shortliffe: MYCIN (1977) (Wed; please focus on first 10 pages, until "templates") and
O'conner et al. 2005
From ISWC '05 proceedings (Wed)

Project #2 due Mon

(No required Catalyt posting on Mon)

Oct 28 OWL & Description logic

Allemang & Hendler text - excerpts from chpts 8, 11 (Mon).
Chpt 8: pp. 153 -171; Chpt 11: pp. 221-237.
GO:Design & implementation, 2001 (Wed) and
Recasting the GO in OWL, 2007 (Wed)

See Matt Horridge's OWL tutorial for Protege4 (15 Meg!)

Nov 4 Resolution & Theorem proving.

Bodenreider & Stevens, 2006: BioOntologies: current trends and future directions (Mon)
No reading due Wed.

Resolution exercise due Wed
Project #3 individual part due FRIDAY

Nov 11
OWL and Open World

No class on Mon (vet's day)
TBD Wed.

Project #3 group part due Wed
Nov 18 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"
Meyer et al., 2004: Application of influence diagrams to prostate IMRT plan selection (Wednesday)

Project #4 check point #1 due Wed
Nov 25 Rules and the Sem Web

Gooch, 2011: Review of challenges for process-oriented HIS. (Monday)

Dec 2 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. .


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:
Sept, '13

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