A major challenge for ontology integration is to deal with inconsistencies. Existing merging tools are based on classical logic and are forced to avoid inconsistencies (to prevent the logic from becoming explosive) which may cause valuable information loss. However, inconsistent information may serve as an integral component in healthcare systems to give a full clinical perspective: any information loss is undesirable. In this paper we discuss various implementation issues for the development of a prototype merging system which will provide an inconsistency-tolerant reasoning mechanism applicable to the healthcare domain.