Reusing medication data is crucial for many medical research domains. Semantic integration of such data in clinical data warehouse (CDW) is quite challenging. Our objective was to develop a reliable and scalable method for integrating prescription data into EHOP (a French CDW). Method: PN13/PHAST was used as the semantic interoperability standard during the ETL process, and to store the prescriptions as documents in the CDW. Theriaque was used as a drug knowledge database (DKDB), to annotate the prescription dataset with the finest granularity, and to provide semantic capabilities to the EHOP query workbench. Results: the system was evaluated on a clinical data set. Depending on the use case, the precision ranged from 52% to 100%, Recall was always 100%. Conclusion: interoperability standards and DKDB, document approach, and the finest granularity approach are the key factors for successful drug data integration in CDW.