Ontology Mapping is the process whereby two ontologies are semantically related at conceptual level and the source ontology instances are transformed into target ontology entities according to those semantic relations. Ontology mapping faces new challenges in the context of Semantic Web, especially concerning heterogeneity, dynamics, distribution and limitations on representation technology. This paper introduces a new methodology and transformation process based on the notion of Service, which represents system transformation capabilities. MAFRA Toolkit is a specific implementation of MAFRA-Mapping FRAmework, where these new methodology and transformation process are being validated. MAFRA Toolkit is being applied in the European project Harmonise, which aims to provide solutions for (semi-) automatic interoperability between major operators in tourism e-business, MAFRA plays a major role in the specification, representation and reconciliation phases of the sematic mapping within the scope of the Harmonise technology.