Structured collection of clinical facts is a common approach in clinical research. Especially in the analysis of rare diseases it is often necessary to aggregate study data from several sites in order to achieve a statistically significant cohort size. In this paper we describe a framework how to approach an integration of heterogeneous clinical data into a central register. This enables site-spanning queries for the occurrence of specific clinical facts and thus supports clinical research. The framework consists of three sequential steps, starting from a formal data harmonization process, to the data transformation methods and finally the integration into a proper data warehouse. We implemented reusable software templates that are based on our best practices in several projects in integrating heterogeneous clinical data. Our methods potentially increase the efficiency and quality for future data integration projects by reducing the implementation effort as well as the project management effort by usage of our approaches as a guideline.
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