This work describes a clinical process management system aimed to support a process-centred vision of health care practices. The system is founded on knowledge representation and semantic information extraction approaches allowing medical knowledge modelling and acquisition. At the heart of the system there are formalisms and languages well suited for representing, clinical processes as workflows, medical and domain knowledge as ontologies and rules enabling the recognition of semantic patterns representing ontology concepts. The system acquires and stores clinical process instances into a medical knowledge base which parameters are obtained exploiting a semantic information extraction approach enabling automatic medical knowledge acquisition from unstructured clinical documents. The main goal of the system is to assists health care professional in executing and monitoring clinical processes by providing functionalities for automatic knowledge acquisition. Acquired information can be analyzed for identifying main causes of medical errors, high costs and, potentially, to suggest clinical processes restructuring or improvement able to enhance cost control and patient safety.