Abstract
The information needed by biologists and physicians for research purposes is distributed over many heterogeneous sources. Integration systems provide a single, centralized and homogeneous interface for users to query multiple information sources simultaneously. The major limitation of integration systems, including mediator-based systems, is that the tasks involved in their creation and maintenance remain mainly manual. To address this limitation, we developed automated methods for facilitating the creation of a mediator-based system. We first implemented an automatic method for acquiring the local schemas of the sources to be integrated. We derived the global schema from the UMLS. Finally, we proposed schema- and instance-based approaches to mapping data elements from the local schemas to the global schema. To illustrate the applicability of our methods, we created a mediator-based system integrating eleven biomedical sources. This prototype is operational, available on the Internet (http://www.med.univ-rennes1.fr/cgi-bin/mougin/These/system.pl) and its evolution is managed semi-automatically.
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.
References
Hernandez, T., Kambhampati, S.: Integration of Biological Sources: Current Systems and Challenges Ahead. In: Proc. ACM SIGMOD Conf., vol. 33(3), pp. 51–60 (2004)
Davidson, S.B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., Stoeckert Jr., C.J.: K2/Kleisli and GUS: experiments in integrated access to genomic data sources. IBM Syst. J. 40(2), 512–531 (2001)
Cohen-Boulakia, S., Davidson, S.B., Froidevaux, C.: A User-Centric Framework for Accessing Biological Sources and Tools. In: Ludäscher, B., Raschid, L. (eds.) DILS 2005. LNCS (LNBI), vol. 3615, pp. 3–18. Springer, Heidelberg (2005)
Stevens, R., Baker, P.G., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., Brass, A.: TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. Bioinformatics 16(2), 184–186 (2000)
Karp, P.D.: A Strategy for Database Interoperation. J. of Comput. Biol. 2(4), 573–583 (1995)
Lindberg, D.A., Humphreys, B.L., McCray, A.T.: The Unified Medical Language System. Methods Inf. Med. 32(4), 281–291 (1993)
McCray, A.T., Srinivasan, S., Browne, A.C.: Lexical methods for managing variation in biomedical terminologies. In: Proc Annu. Symp. Comput. Appl. Med. Care, pp. 235–239 (1994)
Aronson, A.R.: Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In: Proc. AMIA Symp., pp. 17–21 (2001)
Mougin, F., Burgun, A., Loréal, O., Le Beux, P.: Towards the automatic generation of biomedical sources schema. Medinfo. 11(2), 783–787 (2004)
Markowitz, V.M., Chen, I.M., Kosky, A.S., Szeto, E.: Facilities for exploring molecular biology databases on the web: a comparative study. In: Pac. Symp. Biocomput., pp. 256–267 (1997)
Bodenreider, O.: Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. In: Proc. AMIA Symp., pp. 57–61 (2001)
Rahm, E., Bernstein, P.A.: A survey of approaches to automatic schema matching. The International Journal on Very Large Data Bases 10(4), 334–350 (2001)
Shvaiko, P., Euzenat, J.: A survey of schema-based matching approaches. In: Spaccapietra, S. (ed.) Journal on Data Semantics IV. LNCS, vol. 3730, pp. 146–171. Springer, Heidelberg (2005)
Miller, G.A.: WordNet: A Lexical Database for English. ACM Communications 38(11) (1995)
Van Rijsbergen, C.J.: Information retrieval. Butterworth-Heinemann, Newton (1979)
Efthimiadis, E.N.: Query expansion. Annual review of information science and technology 31, 121–187 (1996)
Baker, P.G., Goble, C.A., Bechhofer, S., Paton, N.W., Stevens, R., Brass, A.: An ontology for bioinformatics applications. Bioinformatics 15(6), 510–520 (1999)
Zhang, S., Bodenreider, O.: Alignment of multiple ontologies of anatomy: Deriving indirect mappings from direct mappings to a reference. In: Proc. AMIA Symp., pp. 864–868 (2005)
Sujansky, W.: Heterogeneous database integration in biomedicine. J. Biomed. Inform. 34(4), 285–298 (2001)
Mork, P., Halevy, A., Tarczy-Hornoch, P.: A model for data integration systems of biomedical data applied to online genetic databases. In: Proc. AMIA Symp., pp. 473–477 (2001)
Ben-Miled, Z., Li, N., Liu, Y., He, Y., Lynch, E., Bukhres, O.: On the Integration of a Large Number of Life Science Web Databases. In: Rahm, E. (ed.) DILS 2004. LNCS (LNBI), vol. 2994, pp. 172–186. Springer, Heidelberg (2004)
Köhler, J., Philippi, S., Lange, M.: SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 19(18), 2420–2427 (2003)
Ehrig, M., Sure, Y.: Ontology mapping - an integrated approach. In: Bussler, C.J., Davies, J., Fensel, D., Studer, R. (eds.) ESWS 2004. LNCS, vol. 3053, pp. 76–91. Springer, Heidelberg (2004)
Zhao, H., Ram, S.: Combining schema and instance information for integrating heterogeneous data sources. Data Knowl. Eng. 61(2), 281–303 (2007)
Cohen-Boulakia, S., Davidson, S.B., Froidevaux, C., Lacroix, Z., Vidal, M.E.: Path-based systems to guide scientists in the maze of biological data sources. J. Bioinform. Comput. Biol. 4(5), 1069–1095 (2006)
Kumar, A., Smith, B.: The Unified Medical Language System and the Gene Ontology: Some Critical Reflections. In: Günter, A., Kruse, R., Neumann, B. (eds.) KI 2003. LNCS (LNAI), vol. 2821, pp. 135–148. Springer, Heidelberg (2003)
Miles, A., Matthews, B., Beckett, D., Brickley, D., Wilson, M., Rogers, N.: SKOS: a language to describe simple knowledge structures for the Web. In: XTech 2005: XML, the Web and Beyond (2005)
Baader, F., Calvanese, D., McGuinness, D.L., Nardi, D., Patel-Schneider, P.F. (eds.): The description logic handbook: theory, implementation, and applications. Cambridge University Press, New York (2003)
Maedche, A., Staab, S.: Measuring Similarity between Ontologies. In: International Conference on Knowledge Engineering and Knowledge Management, pp. 251–263 (2002)
Schulz, S., Hahn, U.: Part-whole representation and reasoning in formal biomedical ontologies. Artificial Intelligence in Medicine 34(3), 179–200 (2005)
Doan, A., Madhavan, J., Domingos, P., Halevy, A.: Ontology matching: A machine learning approach. Handbook on Ontologies in Information Systems, 397–416 (2004)
Halevy, A.Y., Ives, Z.G., Suciu, D., Tatarinov, I.: Schema Mediation in Peer Data Management Systems. In: International Conference on Data Engineering, pp. 505–516 (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Mougin, F., Burgun, A., Bodenreider, O., Chabalier, J., Loréal, O., Le Beux, P. (2008). Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds) Data Integration in the Life Sciences. DILS 2008. Lecture Notes in Computer Science(), vol 5109. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69828-9_7
Download citation
DOI: https://doi.org/10.1007/978-3-540-69828-9_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69827-2
Online ISBN: 978-3-540-69828-9
eBook Packages: Computer ScienceComputer Science (R0)