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I just loaded the openCyc OWL file into my OWL editor and found dozens of orphan classes. As the file is so large, it's hard to tell what the problem is, but there does appear to be some classes which are in there twice. They have different IDs, but the same label - one is in the sub-super hierarchy, the other is not. Examples of this are "vehicle bombing" and "appetite", but I suspect there are many more.
I haven't found another OWL editor that can load the file without falling over, so I can't be 100% sure it's not a problem in my OWL Editor. However, from looking at the OWL file in a text editor, there does appear to be some problems.
Hmm. Definitely some glitches in the data, even going to the official site that lets you "look up" words and how they associate. Example - You can find that supernatural entity includes demons, but somehow demons isn't a "thing" in itself, the closest being a car that had the name. Seems like that would have been a big thing to miss. I am guessing that the orphans are something similar, where an association has been made to something else, but the original category has never been looked at again, or mentioned, so Cyc hasn't ever tried to sort out what its connected to properly. Seems like, as much promise as this has, there are serious issues with it too.