I'm using Hermit Reasoner with OWL-API 5 as follows:
OWLOntologyManager manager= OWLManager.createOWLOntologyManager(); //create the manager
OWLOntology ontology=manager.loadOntologyFromOntologyDocument(new File("ontologies/E1G1.owl"));
OWLDataFactory datafact=manager.getOWLDataFactory();
Configuration config= new Configuration();
Reasoner reasoner= new Reasoner(config, ontology);
reasoner.classifyClasses();
reasoner.classifyDataProperties();
reasoner.classifyObjectProperties();
System.out.println(reasoner.isConsistent());
Now I would like to execute SPARQL Query in analogous way as Protégé SPARQL Plugin over the inferred ontology. I'm experimenting JENA ARQ, but it is not clear to me how to integrate them. Any suggestions?