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How do I connect an ontology using java? I have created an ontology using protege. How can I write DL queries in Java to use this ontology?
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You should take a look at the OWL API and Pellet.
DL queries are simply OWL class expressions. You can use the OWL-API as suggested, look at the example provided here. If you need to perform some reasoning in order to retrieve the data of interest, add a reasoner on your classpath (Hermit, Pellet, etc...). You can also think of using the Brain library, developed for this purpose, yet only supporting the OWL2 EL profile at the time being.