Since the approval of the CEN EN13606 norm for the electronic health record communication, a growing interest around the application of this specification has emerged. The main objective of the norm is to serve as a mechanism to achieve the semantic interoperability of clinical data. This will require an effort to use common terminologies, to normalise the clinical knowledge domain and to combine all these formalisations with the existing information systems. This paper presents a methodology and developed tools to reach the seamless semantic interoperability of health data in legacy systems and several study cases where the developed framework has been applied.