At the moment, we are waiting for Protege 5.x to add some key capabilities that are currently only available in Protege 3.5 This means that at the moment, Protege 4 is not supported and will not work with the Essential ontologies and toolset.

I think it's worth pointing out that although Protege 4 is in common use, Protege 3 is still an active product - something that we confirmed with the Protege team a little while ago.

The key capabilities of Protege 3 that are missing from Protege 5 are:

- Multi-user support (that is multiple users working on the ontology concurrently)
- Database backend (we recommend this for large ontologies with thousands of instances)
- Support for Frames based ontologies