In this paper, the aim of automatically generating a cyber-physical control system (more precisely, an IEC61499 control system) is discussed. The method is enabled by ontology models, specifically the source plant ontology model and the target control model for the CPS system implemented in the preferred programming language. The transforming of ontologies is enabled by an extension of SWRL (called eSWRL) and it is introduced here. There interpreter of eSWRL is developed using the Prolog language. A case study Baggage Handling System is used to demonstrate how the ontology models are transformed and the corresponding transforming rules that are developed.