Abstract Ontologies are helpful in giving interoperable structures to sources of knowledge and information. This interoperability, however, is greatly hindered by the heterogeneity of independently developed ontologies which in turn increases the requirements for mediation systems to reconcile the differences. A core concepts ontology for a certain domain contained by a foundation ontology can be used to alleviate this problem and to facilitate the reconciliation efforts. Possible differences in the use of concepts from the core concepts to model entities in domain ontologies can be prevented by binding the domain ontology developers to some rules. These rules can be particularly useful for domain ontologies requiring some kind of traceability of their concepts in the foundation ontology. The mediation system can then use this traceability to establish similarities between two ontologies. Software applications, like the one explained in this paper, can then be developed to perform the mediation task automatically and accurately.