A clinical decision support system, based on rules described in the semantic web rule language and with semantic annotations from biomedical and time ontologies, is used to reason on processes modeled in the business process modeling notation. This paper, as a case study within the framework of functional rehabilitation processes, analyzes the modeling of the rehabilitation activity consisting of improving the upper limb functioning of patients. The clinical decision support system provides personalization of therapies and is powerful enough to deal with the special characteristics of a rehabilitation scenario, which includes several types of indicators, medical ontologies, and time annotations of different granularities. This paper presents the main lines of a rule-based, ontological framework to translate informal, descriptive methods about functional rehabilitation with an intuitive semantics to the formal representation needed by computational systems. A rule-based reasoning system is used for the representation of processes' semantics and the modeling categories are based on well-accepted rehabilitation notions. We believe that the solution presented for functional rehabilitation can be generalized to other rehabilitation domains such as respiratory, cognitive and cardiac rehabilitation.