Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System

  • Authors:

  • Fleur Mougin;Anita Burgun;Olivier Bodenreider;Julie Chabalier;Olivier Loréal;Pierre Beux

  • Affiliations:

  • EA 3888, IFR 140, Faculté de Médecine, University of Rennes 1, France and LESIM, INSERM U593, ISPED, University of Bordeaux 2, France;EA 3888, IFR 140, Faculté de Médecine, University of Rennes 1, France;National Library of Medicine, Bethesda, Maryland, USA;EA 3888, IFR 140, Faculté de Médecine, University of Rennes 1, France;INSERM U522, IFR 140, University of Rennes 1, CHU Pontchaillou, France;EA 3888, IFR 140, Faculté de Médecine, University of Rennes 1, France

  • Venue:
  • DILS '08 Proceedings of the 5th international workshop on Data Integration in the Life Sciences
  • Year:
  • 2008

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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.