This is going to be a short post. I imagine most people who read this will already know but just in case some don't I wanted to let people know there is a new version of Protégé from Stanford. It can be downloaded from the Protégé web site: https://protege.stanford.edu/ Just go to that page and click on the red "Download Now" button and it will take you to the appropriate link for the latest version (5.6) for your OS. I've been using the new version and I really like it. Just a couple points about my experience:
Use Pellet. I started using Hermit because that is one of the default reasoners that comes bundled with Protégé (the other is Elk which I think is very fast but doesn't support all of the OWL2 spec) so I thought I would give Hermit a try. I usually use Pellet because I like using SWRL (although I recently found out I've been essentially using the wrong SWRL UI, more on that to come). But I found Hermit to be slow on just small to medium ontologies. When I installed the Pellet plugin, an ontology that was taking several seconds for the reasoner to run with Hermit ran in less than a second with Pellet so I think it is worth downloading the Pellet plugin even if you don't use SWRL.
UI Bug Fixed! This is the most important fix. In 5.5 when I encountered an error in the reasoner the UI would often lock up and I would have to force quit and then restart Protégé. I'm not sure if this was a Windows bug or a Pellet bug but even though I don't think it happened to everyone it happened to me a lot. This was a major pain. In previous versions that almost never happened. It fundamentally changed the way I used the reasoner. Whereas before I would run the reasoner all the time, with 5.5 I was very cautious about running the reasoner and when I expected I might get an error would be careful to save my work before I ran it. That bug seems to be fixed and now the reasoner works as it should. Not only does it not lock up but it usually points you right to the axiom(s) that are causing an inconsistency.
Also, for those who aren't already aware, the Protégé user support group provides great support. You can register here: https://protege.stanford.edu/support.php Click on the first red button next to Protégé User Support.