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

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 mul-tiple 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 map-ping data elements from the local schemas to the global schema. To illustrate the applicability of our methods, we created a mediator-based system integrat-ing eleven biomedical sources. This prototype is operational, available on the Interne