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Semantic collision is inevitable while building a domain ontology from heterogeneous data sources (semi-)automatically. Therefore, the semantic consistency is indispensable precondition for building a correct ontology. In this paper, a model-checking-based method is proposed to handle the semantic consistency problem with a kind of middle-model methodology, which could extract a domain ontology from structured and semistructured data sources semiautomatically. The method translates the middle model into the Kripke structure, and consistency assertions into CTL formulae, so a consistency checking problem is promoted to a global model checking. Moreover, the feasibility and correctness of the transformation is proved, and case studies are provided.