Medical routine data has the potential to benefit research. However, transferring this data into a research context is difficult. For this reason Medical Data Integration Centers are being established in German university hospitals to consolidate data from primary information systems in a single location. But, small data-sets from one organization can be insufficient to answer a research question adequately. In order to obtain larger data-sets, attempts to merge and provide data-sets across institutional boundaries are made. Therefore, this paper proposes a possible process that can extract, merge, pseudonymize and provide distributed data-sets from several organizations conforming to privacy regulations. This process is executed according to the open standard BPMN 2.0, the underlying process data model is based on HL7 FHIR R4. The proposed solution is currently being deployed at eight university hospitals and one Trusted Third Party in the HiGHmed consortium.