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Ontology integration is an important task which needs to be performed when several information systems share or exchange knowledge. We consider that most of previous methods of ontology integration merely involve blind or exhaustive matching among all concepts belonging to different ontologies. Therefore, semantic mismatches, logical inconsistencies and conceptual conflicts between ontologies are unavoidable. Additionally, the computational complexity increases rapidly in integrating large ontologies. This research aims at investigating an effective methodology for ontology integration, in which, a propagating inconsistency algorithm has proposed to reduce complexity and mismatching in ontology integration. A reconciled algorithm is suggested to generate a best representation from conflict concepts. In evaluation, we compare our complexity of the algorithms and accuracy of the results with previous approaches'.