As a general rule, basic is going to be the stuff you mine, such as granum. Intermediate is the stuff you get from running the raw stone through a single extraction station, such as amerantum(sp?). Advanced is going to be the stuff you get from extracting intermediate things, such as waterstone.
I'm not 100% sure the above statement is correct as in beta skills went up so fast we barely paid attention to what was raising them. That being said, it holds true with the extraction I've done since release and I THINK it's the way it works.