One of the most challenging problems in the healthcare domain is providing interoperability among healthcare information systems. In order to address this problem, we propose the semantic mediation of exchanged messages. Given that most of the messages exchanged in the healthcare domain are in EDI (Electronic Data Interchange) or XML format, we describe how to transform these messages into OWL (Web Ontology Language) ontology instances. The OWL message instances are then mediated through an ontology mapping tool that we developed, namely, OWLmt. OWLmt; uses OWL-QL engine which enables the mapping tool to reason over the source ontology instances while generating the target ontology instances according to the mapping patterns defined through a GUI.