As scientific achievements in the area of Healthcare have evolved during the last decade, inevitably there has been an increase of treatment quality. One of the challenges to be confronted is the personalization of treatment since each patient constitutes a unique case. The personalization requires the continuous reconfiguration of the treatment schemes since the clinical status of each patient and circumstances inside a healthcare organization constantly change. In this paper we present a holistic software environment that provides an IT solution concerning the real-time adaptation of healthcare processes. The software comprises a healthcare process execution engine assisted by a semantic info-structure for reconfiguring the pathways. The semantic info-structure utilizes an ontology enclosing the required knowledge and a semantic rule-set. During the execution of clinical pathways, the system reasons over the rules, the knowledge and information, and reconfigures the next steps of the treatment. The results of the rule-set execution may generate knowledge objects to be inserted in the ontology. A graphical designer is provided for the definition of the rule-set for the clinical pathways adaptation.