Abstract
Currently, knowledge from biological research is stored in hundreds of databases, counting only public accessible ones. Finding specific data in these is a challenging task which can be supported by ontologies describing them. The maintenance of a corresponding ontology is time consuming manual work, because research database schemas change rapidly. Our project will reduce the work by automating tasks, like a generation process and applying schema changes to the corresponding ontology. We call the proposed method coevolution, because database schema and ontology are allowed to evolve independently without ever losing their connection to each other. Our method consists of initial ontology generation, manual annotation and change propagation steps.
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
Spyns, P., Meersman, R., Jarrar, M.: Data modelling versus ontology engineering. SIGMOD Rec. 31, 12–17 (2002)
Erdmann, M., Studer, R.: How to structure and access XML documents with ontologies. Data Knowl. Eng. 36, 317–335 (2001)
Bechhofer, S., van Harmelen, F., Hendler, J., Horrocks, I., McGuinness, D., Patel-Schneider, P., Stein, L.: OWL web ontology language reference, W3C (2004)
Gómez-Pérez, A., Fernández-López, M., Corcho, O.: Ontological Engineering. Springer, Heidelberg (2004)
de Laborda, C., Conrad, S.: Relational.OWL - A Data and Schema Representation Format Based on OWL. In: Conceptual Modelling 2005 (APCCM 2005), pp. 89–96. Australian Computer Society (2005)
Galperin, M.Y.: The Molecular Biology Database Collection: 2006 update. Nucl. Acids Res. 34, D3–D5 (2006)
Lacroix, Z., Critchlow, T.: Bioinformatics – Managing Scientific Data. Morgan Kaufmann, San Francisco (2003)
Stevens, R., Wroe, C., Lord, P., Goble, C.: Ontologies in Bioinformatics. In: Int. Handbooks on Information Systems, pp. 635–657. Springer, Heidelberg (2004)
Fan, H., Poulovassilis, A.: Schema evolution in data warehousing environments - a schema transformation-based approach. In: Atzeni, P., Chu, W., Lu, H., Zhou, S., Ling, T.-W. (eds.) ER 2004. LNCS, vol. 3288, pp. 639–653. Springer, Heidelberg (2004)
Tresch, M.: Evolution in Objekt-Datenbanken. Teubner, Stuttgart (1995)
Lu, J.J., Hsu, C.N.: Query answering using ontologies in agent-based resource sharing environment for biological web information integrating. In: Proc. of IJCAI 2003 Workshop on Information Integration on the Web, pp. 197–202 (2003)
Stuckenschmidt, H., van Harmelen, F.: Information Sharing on the Semantic Web. In: Advanced Information and Knowledge Processing. Springer, Heidelberg (2005)
Castano, S., Antonellis, V.D.: A Discovery-Based Approach to Database Ontology Design. Distrib. Parallel Databases 7, 67–98 (1999)
Kroenke, D.: Database Processing. Fundamentals, Design, and Implementation, 10th edn. Pearson Prentice Hall, New Jersey (2005)
Franconi, E., Grandi, F., Mandreoli, F.: Schema evolution and versioning: A logical and computational characterisation. In: Balsters, H., De Brock, B., Conrad, S. (eds.) FoMLaDO 2000 and DEMM 2000. LNCS, vol. 2065, pp. 85–99. Springer, Heidelberg (2001)
Ding, Y., Foo, S.: Ontology research and development, Part 2 - A review of ontology mapping and evolving. Journal of Information Science 28, 375–388 (2002)
Knublauch, H., Fergerson, R., Noy, N., Musen, M.: The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 229–243. Springer, Heidelberg (2004)
Noy, N.F., Klein, M.: Ontology evolution: Not the same as schema evolution. Knowl. Inf. Syst. 6, 428–440 (2004)
Necib, C.B., Freytag, J.: Query Processing Using Ontologies. In: Pastor, Ó., Falcão e Cunha, J. (eds.) CAiSE 2005. LNCS, vol. 3520, pp. 167–186. Springer, Heidelberg (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kupfer, A., Eckstein, S., Neumann, K., Mathiak, B. (2006). Handling Changes of Database Schemas and Corresponding Ontologies. In: Roddick, J.F., et al. Advances in Conceptual Modeling - Theory and Practice. ER 2006. Lecture Notes in Computer Science, vol 4231. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11908883_28
Download citation
DOI: https://doi.org/10.1007/11908883_28
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-47703-7
Online ISBN: 978-3-540-47704-4
eBook Packages: Computer ScienceComputer Science (R0)