Abstract
Within the post-genomic era, scientists want to exploit the information of genome sequencing results, protein interactions, and gene deleted phenotypes. Molecular biologists build ontologies to model their knowledge in non-ambiguous ways. Ontologies are metadata describing the meaning of data. They are useful for query answering in databases, hypotheses testing, and for the rep-resentation of context or explanation models. The provision of ontologies of complex information is challenging. Ontological Design Patterns (ODPs) make the ontological structure and content explicit. ODPs can be traced to reuse and adapt ontologies to objectives of information search, analysis and comparison. The three ODPs shown in this paper provide methods to hide unnecessary in-formation (InteractionHider ODP), to notify interdependent concepts if one concept is changed (UpdateDependency ODP), and to handle multiple concepts, that can fulfil a specific context (ChainOfConcept ODP). All ODPs are avail-able from the author with code examples. Contact: reich@cs.man.ac.uk
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Toberts, K.; Watson, J. D. (1994). Molecular Biology of the Cell. 3rd ed. Garland Publishing, Inc. New York, London
Alexander, Chr. (1979). The Timeless Way of Building, Oxford University Press
Bench-Capon, T. (1998). The Role of Ontologies in the Verification and Validation of Knowledge based Systems. Proceedings of the 9th International Workshop on Database and Expert Systems, 64–69. Los Alamitos, IEEE Press
Beys, P.; Benjamins, R.; Van Heijst, G. (1996). Remedying the reusability-usability trade-off for problem-solving methods. Proceedings of the Tenth Knowledge Acquisition Work-shop (KAW96)
Calvanese, D.; De Giacomo, G.; Lenzerini, M.; Nardi, D.; Rosati, R. (1998). Description logic framework for information integration. Proceedings of the sixth International Conference on the Principles of Knowledge Representation and Reasoning (KR-98): 2–13
Coad, P. (1992). Object-oriented Patterns. Communications of the ACM. 35(9):152–159
Coplien, J.O. (1992). Advanced C++ Programming Styles and Idioms. Addison-Wesley, Reading, MA
Craven, M.; Kumlien, J. (1999). Constructing biological knowledge bases by extracting information from text sources. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. Heidelberg, Germany:77–86
Gamma E., Helm R., Johnson R., Vlissides J. (1994). Design Patterns-Elements of Reusable Object-Oriented Software. Addison-Wesley
Gruber, Th. R. (1995). Toward principles for the design of ontologies used for knowledge sharing. International Journal Human-Computer Studies 43, 907–928
Horrocks, I. R. (1998). Using an expressive description logic: FaCT or Fiction? Proceedings of the sixth International Conference on the Principles of Knowledge Representation and Reasoning (KR-98)
Neches, R.; Fikes, R.; Finin, T.; Gruber, T.; Patil, R.; Senator, T.; Swartout, W. (1991). Enabling technology for knowledge sharing. AI Magazine: 36–56
Oliver, S. (1996). From DNA sequence to biological function. Nature, 379:597–600.
Prekas, N.; Loucopoulos, P.; Roland, C.; Grosz, G.; Semmak, F.; and Brash, D. (1999). Developing Patterns as a Mechanism for Assisting the Management of Knowledge in the Context of Conducting Organisational Change. Proceedings of the 10th International Conference, DEXA’99, Florence Italy, Lecture Notes in Computer Science 1677, Springer Verlag
Reich, J.R. (2000 b). Modelling Molecular Biological Information: Ontologies and Onto-logical Desing Patterns. IRMA 2000, 21–24 May, Anchorage, Alaska 166 http://www.irma-international.org/call2000.htm
Reich, J.R. (2000 a). Ontological Design Patterns for the Management of Molecular Bio-logical Knowledge. AAAI 2000, 20–22 March, Stanford, CA, USA (http://www.aifb.uni-karlsruhe.de/~sst/Research/Events/sss00/)
Reich, J.R. (1999 b). Molecular Biological Ontologies and Ontological Design Patterns: What they are, and how they look like. IEE Informatics, Two-day Seminar’ Searching for information: artificial intelligence and information retrieval approaches’, 11–12. November, Glasgow, Great Britain: 12-1–12-3
Reich, J. R. (1999 a). Ontological Design Patterns for the Integration of Molecular Bio-logical Information. Proceedings of the German Conference on Bioinformatics (GCB’99): 156–165, Hannover, Germany, (http://www.bioinfo.de/isb/gcb99/talks/reich)
Robbins, R. J. (1996). Comparative Genomics: a new Integrative Biology. In: Julio Col-lado-Vides, Boris Magasanik, Temple F. Smith (eds.). Integrative Approaches to Molecular Biology, The MIT Press, Cambridge: 63–90
Steele, G. L., Jr. (1990). Common Lisp the Language, 2d edition. Digital Press
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Reich, J.R. (2000). Ontological Design Patterns: Metadata of Molecular Biological Ontologies, Information and Knowledge. In: Ibrahim, M., Küng, J., Revell, N. (eds) Database and Expert Systems Applications. DEXA 2000. Lecture Notes in Computer Science, vol 1873. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44469-6_65
Download citation
DOI: https://doi.org/10.1007/3-540-44469-6_65
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-67978-3
Online ISBN: 978-3-540-44469-5
eBook Packages: Springer Book Archive