referencedEntities.addAll( ontology.getIndividualsInSignature() );
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for( OWLAxiom axiom : ontology.getAxioms() ) {
if( !axiom.isLogicalAxiom() ) {
changes.add( new RemoveAxiom( ontology, axiom ) );
}
}
manager.applyChanges( changes );