I'm building a mid-size ontology with only 5 SWRL rules. Every time I run my SWRL rules and try to transfer the inferred axioms to the ontology, my class hierarchy gets changed a lot. Subclasses become sibling classes to what were previously their superclasses, even though when I check the info tab, theyre still marked as subclasses properly.
On the 'Inferred' tab of the class hierarchy, things stay in order, but the asserted tab gets really messy.
Further, my SWRL rules are only ~50% effective; many individuals which satisfy the antecedent dont seem to be affected by running the rules. I went through each of these individuals, and I cant seem to find anything in common that would be making things go wrong.
I've tried a few different reasoners, but ELK seems to be the only one which can reason through the ontology in less than a minute (Pellet was taking around 10). But every reasoner had the same issue.
I'm also using protege 5.6.1