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Summary

Summary. A definition of ontology as a characterisation of conceptualisation -- capturing the things we know about a domain; The knowledge within an ontology can be applied to a variety of tasks;

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Summary

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  1. Summary • A definition of ontology as a characterisation of conceptualisation -- capturing the things we know about a domain; • The knowledge within an ontology can be applied to a variety of tasks; • A survey of current bio-ontologies showing use as controlled vocabulary, schema definition and query formulation; • Building an ontology -- process and life-cycle; • Influences on the choice of encoding language; • The desirability of tools for the building, management and exchange of ontologies;

  2. Final remarks • The use of ontologies is growing within the bio-molecular world • They are a high-cost, but high-benefit solution to a variety of problems confronting the bioinformatics community.

  3. Some References (1) Review • Stevens R., Goble C.A. and Bechhofer, S. Ontology-based Knowledge Representation for Bioinformatics accepted for Briefings in Bioinformatics Bio-ontologies & Systems • Karp P. D. An ontology for biological function based on molecularinteractions Bioinformatics 2000;16 269-285 • Ashburner et al Gene Ontology: Tool for the Unification of Biology, Nature Genetics Vol 25 pages 25-29 • R. Altman, M. Bada, X.J. Chai, M. Whirl Carillo R.O. Chen, and N.F. Abernethy. RiboWeb: An Ontology-Based System for Collaborative Molecular Biology. IEEE Intelligent Systems, 14(5):68-76, 1999. • P.G. Baker, C.A. Goble, S. Bechhofer, N.W. Paton, R. Stevens, and A Brass. An Ontology for Bioinformatics Applications. Bioinformatics, 15(6):510-520, 1999. • R.O. Chen, R. Felciano, and R.B. Altman. RiboWeb: Linking Structural Computations to a Knowledge Base of Published Experimental Data. In Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, pages 84-87. AAAI Press, 1997. • P. Karp and S. Paley Integrated Access to Metabolic and Genomic Data Journal of Computational Biology, 3(1):191--212, 1996. • P. Karp, M. Riley, S. Paley, A. Pellegrini-Toole, and M. Krummenacker. EcoCyc: Electronic Encyclopedia of phE. coli Genes and Metabolism. Nucleic Acids Research, 27(1):55-58, 1999. • S. Schulze-Kremer. Ontologies for Molecular Biology. In Proceedings of the Third Pacific Symposium on Biocomputing, pages 693-704. AAAI Press, 1998. • P.G. Baker, A. Brass, S. Bechhofer, C. Goble, N. Paton, and R. Stevens. TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. An Overview. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 25--34. AAAI Press, June 28-July 1, 1998 1998.

  4. Some References (2) Ontology development and exchange • T.R. Gruber. Towards Principles for the Design of Ontologies Used for Knowledge Sharing. In Roberto Poli Nicola Guarino, editor, International Workshop on Formal Ontology, Padova, Italy, 1993. Available as technical report KSL-93-04, Knowledge Systems Laboratory, Stanford University:ftp.ksl.ftanford.edu/pub/KSL_Reports/KSL-983-04.ps. • I. Horrocks, D. Fensel, J. Broekstra, M. Crubezy, S. Decker, M. Erdmann, W. Grosso, C. Goble, F. Van Harmelen, M. Klein, M. Musen, S. Staab, and R. Studer. The ontology interchange language oil: The grease between ontologies. http://www.cs.vu.nl/ dieter/oil. • R. Jasper and M. Uschold A Framework for Understanding and Classifying Ontology Applications. In Twelfth Workshop on Knowledge Acquisition Modeling and Management KAW'99, 1999. • M. Uschold and M. Gruninger. Ontologies: Principles, Methods and Applications. Knowledge Engineering Review, 11(2), June 1996.

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