Supporting medical processes is among the most difficult endeavors. In contrast to uniform and unvaried workflows, the complexity and dynamics of patient treatment processes prevents the application of standard methodologies and tools, such as workflow systems. Despite long-term research in flexible and adaptive workflows as well as computerized clinical guidelines there are hardly any applications used in clinical routine. However, Standard Operation Procedures are a key element for any hospital to continuously improve their processes with regard to quality of patient care as well as resources required. Based on a three-level representation of know-how about patient care and treatment, we present a methodology for a stepwise formalisation and automation of clinical guidelines embedded into a patient data management system.