Yes you are definitely right! One has to use Protege 3.5 to author rules and Protege >=4 to execute them on an OWL 2 ontology. However, one more reason is the introduction of SPIN rules, i.e. SPARQL CONSTRUCT expressions that are stored within the ontology. And tools such as TopBraid composer can be used to run these rules. Of course, ontologies must be in the OWL 2 RL profile, namely a rule-equivalent subset of OWL, so that OWL2 RL reasoning can be combined with user-defined rules in SPIN.
Hi, I'am using a private ontology with more than 500 SWRL rules. We had a lot of challenges, but at the end of the day I can summarise, that you can edit and run such an amount of rules with Protégé Version 5 and the SWRL Tab Plugin developed by O'Connor.
It would be interesting for me to test the conversion of such a big rule-base into an equivalent rule-base of SPIN-SPARQL rules and/or SHACL rules. I have developed a Prolog-based tool for this:
It is possible to generate rules from pure OWL ontologies. Please, see "Evolution of ontology potential for generation of rules" and "Ontology as a source for rule generation".