N. Noy & D. L. McGuinness. Ontology Development 101: A Guide to Creating Your First Ontology. Stanford Medical Informatics TR #SMI-2001-0880, 2001. (due Wed.)

Davis, R., Shrobe, H., & Szolovitz, P. (1993). What is a knowledge representation? AI Magazine, Spring, pp. 17-33. (due Wed.)

Ontology building exercise due on Monday! (part 1) See assignment specification.

A. L. Rector, J. Rogers (1999). Ontological issues in using a description logic to represent medical concepts: Experience from GALEN. IMIA WG6 Workshop: Terminology and Natural Language in Medicine. Phoenix Arizona, Nov 1999.

Rosse, C. and Mejino, J. L. V. (2003) A Reference Ontology for Bioinformatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics 36:478-500.

Davis, R., Buchanan, B.G., & Shortliffe, E.H. (1977) Production rules as a representation for a knowledge-based consultation program. Artificial Intelligence 8: 15-45. Reaction Paper Reading!!

Hripcsak, Ludeman, Pryor, Wigertz, & Clayton (1994). Rationale for the Arden Syntax. Computers and Biomedical Research 27: 291-324.

D Wang, M Peleg, S W. Tu, A A. Boxwala, R A. Greenes, V L. Patel, and E H. Shortliffe (2002). Representation primitives, process models and patient data in computer-interpretable clinical practice guidelines: A literature review of guideline representation models, International Journal of Medical Informatics 68: 59-70. (due Wed)

Ontology building exercise due on Monday! (part 2) See assignment specification

Peter D. Karp (2000). An ontology for biological function based on molecular interactions Bioinformatics 16: 269-285.

The Gene Ontology Consortium (2001). Creating the gene ontology resource: design and implementation. Genome Research 11: 1425-1433. Also, download the entire ontology ("GO") into Protege for your viewing pleasure.

A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OIL C.J. Wroe, R. Stevens, C.A. Goble, M. Ashburner; Pacific Symposium on Biocomputing 8:624-635 (2003). (due Wed)

Iwei Y., Karp, P., Noy, N., & Altman, R. (2003) Knowledge acquisition, consistency checking, and concurrency control for Gene Ontology (GO). Bioinformatics, 19(2): 241 - 248. (due Wed)

Hendler, J. (2001) Agents and the semantic web. IEEE Intelligent Systems (special issue on the Semantic Web) 16(2): 30-37. Reaction Paper Reading!!

Berners-Lee, T., Hendler, J. & Lassila, O. (2001). The Semantic Web. Scientific American, May 17th. Note: the e-res version is plain html, with no Figures. A web version of the paper is available, with links to Figures. Also, for more on the semantic web, see: http://www.semanticweb.org/

Knublauch, H., Dameron, O., & Musen, M. (in press). Weaving the biomedical semantic web with the Protege OWL plug-in. Workshop on formal biomedical knowledge representation (KR-MED), Whistler, CA. (Optional reading due Wed)

Stevens, R.; Goble, C.; Horrocks, I.; Bechhofer, S. (2002). OILing the way to machine understandable bioinformatics resources IEEE Transactions on Information Technology in Biomedicine 6(2): 129-134. (due Wed)

Guest lecture Wednesday by Peter Mork: XML, RDFS, and the semantic web.

Cimino, J.J., Clayton, P.D., Hripscak, G., and Johnson, S.(1994). Knowledge-based approaches to the maintenance of a large controlled medical terminology. Journal of the American Medical Informatics Association (JAMIA). 1(1): 35-50.

The Nat'l Library of Medicine, Documentation: 2002 UMLS Semantic Network. available at http://www.nlm.nih.gov/research/umls/META3.HTML#s3

Campbell, K., Oliver, D., and Shortliffe, E. (1998) The Unified Medical Language System: Toward a collaborative approach for solving terminologic problems. Journal of the American Medical Informatics Association. 5(1): 12-16. (Optional)

Towards a Broad-Coverage Biomedical Ontology Based on Description Logics U. Hahn, S. Schulz; Pacific Symposium on Biocomputing 8:577-588 (2003). (Due Wed)

Final project topic choice due on Mon. See final project assignment.

Levesque, H.J., and Brachman, R.J. (1987). Expressiveness and tractability in knowledge representation and reasoning. Computational Intelligence, 3: 78-93. Also available in Readings in Knowledge Representation, Brachman, R.J. & Levesque, H.J., Eds. (1985), Morgan Kaufman.

Quiz Wednesday on theorem-proving & logics.

Lecture on Resolution theorem proving - "Deductive Databases", Horn clauses, and/or Prolog (??)

Neches, R., Fikes, R. E., Finin, T., Gruber, T.R., Patil, R., Senator, T., and Swartout, W. R. (1991). Enabling technology for knowledge sharing. AI Magazine, 12(3), 16–36.

Altman, R.B., Bada, M., Chai, X.J., Carillo, M.W., Chen, R.O., Abernathy, N.F. (1999) RiboWeb: An ontology-based system for collaborative molecular biology. IEEE Intelligent Systems. 14(5): 68-76. Reaction Paper Reading!!

Chaudhri, V.K., Farquhar, A., Fikes, R., Karp, P.D., Rice, J., (1998). OKBC: A programmatic foundation for knowledge-base interoperability. In Proceedings of the Fifteenth National Conference on Artificial Intelligence (AAAI-98), pp. 600-607, Madison, Wisconsin.

Final project checkpoint due on Mon. See final project assignment.

MacGregor, R., (1991). The Evolving Technology of Classification-Based Knowledge-Representation Systems. In J. Sowa (ed.), Principles of Semantic Networks, Morgan Kaufmann. (due Wed.)
See also the Ontosaurus/LOOM web page

Matthew Richardson & Pedro Domingos (2003). Building Large Knowledge Bases by Mass Collaboration Proceedings of the 2nd International Conference on Knowledge Capture (K-CAP '03). pp. 129-137.

(Monday is memorial day)

Readings on the CYC project:
Guha, R.V. & Lenat, D.B. (1994). Enabling agents to work together. Communications of the ACM, 37(7): 127-142.

Reading on Project Halo:
Noah S. Friedland, Paul G. Allen, and many, many others (in press). Towards a Quantitative, Platform-Independent Analysis of Knowledge Systems. Proceedings of the 9th International Conference on Principles of Knowledge Representation and Reasoning (KR-2004).

Student final project presentations