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How does the closed world assumption of Prolog (if it's not explicitly specified it is assumed false) mesh with the open world assumption (if it is not explicitly specified it is unknown) of RDF?

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In all the practical applications I've seen of RDF or OWL, all the queries rely on some form of the closed-world assumption.

OWA exists only on paper. Practically all implementations assume CWA.

That's false. Several practical implementations of OWL and RDF are based on OWA. At least one is based on CWA and OWA.

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