Data integration is an important task in medical informatics and highly impacts the gain out of existing health information data. These tasks are using implemented as extract transform and load processes. By introducing HL7 FHIR as an intermediate format, our aim was to integrate heterogeneous data from a German pulmonary hypertension registry into an OMOP Common Data Model. First, domain knowledge experts defined a common parameter set, which was subsequently mapped to standardized terminologies like LOINC or SNOMED-CT. Data was extracted as HL7 FHIR Bundle to be transformed to OMOP CDM by using XSLT. We successfully transformed the majority of data elements to the OMOP CDM in a feasible time.