I foolishly entered a lot of data into a new ontology without saving for a while. I then realized that one of my data properties that should have been functional wasn't defined that way so I checked the functional box and ran the Reasoner. I got an error because one of my individuals has two values for that property. Unfortunately, the inconsistency wasn't handled very well. My Protege screen is all messed up (see attached image) and I can't click on the File menu option to save the ontology. I was able to click on Window>Refresh current window but it didn't do anything and now I can't click on anything.
If I could save the ontology, it would be fine, I know which individual has the error and I could restart Protege, load the ontology and then edit the individual before I run the Reasoner. But I can't figure out how to save the ontology because none of the menu options are responding anymore. I'm using 5.5. on Windows with the Pellet reasoner. I'll probably just have to bite the bullet and kill Protege then restart it, reload the last saved version and redo the work but just in case there is some option I haven't thought of I thought I would post here first. Also, thought you would like to know since this isn't a very good way to handle an inconsistent ontology.