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University of Washington."},{"key":"ref16","unstructured":"Bechhofer S, van Harmelen F, Hendler J, Horrocks I, McGuinness DL, <etal>et al<\/etal>.. (2004) OWL Web Ontology Language Reference. W3C recommendation. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.w3.org\/TR\/owl-features\/\" xlink:type=\"simple\">http:\/\/www.w3.org\/TR\/owl-features\/<\/ext-link>. 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