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) |
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| Sept 30 | What are the data? Sharing data... Querying data |
Allemang & Hendler text - chpt 3: RDF (Wed) |
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| Oct 7 | More querying |
Ontology Development 101, thru the end of section 3 (Mon) |
Project #1 due Wed |
| Oct 14 | Inference, logics, |
Demir et al, 2010 (Mon) |
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| 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) |
Project #2 due Mon (No required Catalyt posting on Mon) |
| Oct 28 | OWL & Description logic | Allemang & Hendler text - excerpts from chpts 8, 11 (Mon). |
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) |
Resolution exercise due Wed |
| Nov 11 | OWL and Open World |
No class on Mon (vet's day) |
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" |
Project #4 check point #1 due Wed |
| Nov 25 | Rules and the Sem Web | Gooch, 2011: Review of challenges for process-oriented HIS. (Monday) |
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| 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. .
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:
Sept, '13
Contact the instructor at: gennari@uw.edu