In this paper an ontology driven approach to the design of control systems, in particular, control applications of IEC 61499 standard is proposed. The source ontology is an ontological description of control object (plant) while the target ontology is an ontological description of a control system implemented using an appropriate programming language. For the ontologies transformation an extension of SWRL (called eSWRL) is informally introduced. Interpretation of eSWRL constructs is implemented using Prolog language. An example of transformation of the ontological description of a baggage handling system to the ontological description of a control application based on IEC 61499 function blocks (FB) is in detail considered. The corresponding transformation rules have been developed in the context of this example.