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The ontology model of software engineering is an effective approach for the intercommunion between people from the different domains, the communication and interoperation among agents, and the share and reuse of the software. But the lack of formal analysis tools for domain modeling results in taking liberties with conceptualization. This paper discusses how to introduce the ontological notions from philosophy into knowledge representation of software engineering in order to supply a set of formal analysis tools for conceptualization analysis. This method can definitely record the hypothesis and analysis criterions through ontology building, and clarify the hierarchy of concepts for multisite software.