I got sidetracked last night and didn’t post this as I finished the work. I was having trouble creating individuals within the Protege 3.4.4 API, so I did a little research to see if I could find a solution. In the process, I came across the Manchester OWL API, which it just so happens is the API that Protege 4.x is based on.

The Manchester API is somewhat more verbose, but that’s due it it taking more of what I would call a “purist” approach to building the ontology. Instead of inserting a class, you make an  assertion about the class and add the assertion to the ontology. It’s a little confusing at first, but I got the hang of it pretty quickly.

The end result of all this is that I now have an ontology that is populated with individuals that are part of the appropriate parameter subclass. And just in time for a meeting with my adviser this afternoon.