Sounds fine, store the hierarchy but keep it separate from the items. No worries. The idea of supporting multiple hierarchies for different inheritances is interesting and I can see its potential importance. I'll need to test it out here in "biology land" to see if it makes sense in practice.

I believe that the classification is tied very closely to taxon concepts, and that descriptions are certainly tied to concepts. If you change the concept you almost always change the description, and so knowing the classification can be important in understanding what the author is up to.

Steve