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In fact my problem that I create a tool for developing ontology automatically. Then I want to evaluate the ontology given by my tool but I want to automatically evaluate it. Could anyone please suggest for me a good tool to do it ?

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Consistency is a standard check that any reasoer can perform, you only have to pick an api to use one. For Java, you can use Jena or OWL API. Various reasoners exist, e.g., Pellet, HermiT, FaCT++ - the list is long.

"Clear and error free and covers the domain" - this is hard to quantify. Depends on the domain, your intended use and your definition of clear.

Ignazio
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