Clinical guidelines systematically assist practitioners to provide an appro- priate health care in specific clinical circumstances. A significant number of guide- lines and protocols is lacking in quality. Indeed, ambiguity and incompleteness are likely anomalies in medical practice. In order to find anomalies and to improve the quality of medical protocols, this paper presents a stepwise formal development of a medical protocol. In this development, we define the domain concepts based on ontology to integrate with the medical protocol in an explicit way. In this work, we use the Event B language for modeling a domain model using ontologies and to cap- ture the functional behaviour of the medical protocol. Our main contributions are: to use the domain specific knowledge in a system model explicitly; to link between the domain model and system model using an annotation mechanism; and to use the proof based formal approach to evaluate a medical protocol. An assessment of the proposed approach is given through a case study, relative to a real-life reference pro- tocol (ECG interpretation), which covers a wide variety of protocol characteristics related to different heart conditions.