We are moving from practical designs and implementations of ontologies in systematics to design theory. One issue to understand, or least have an intuitive position on, is the strength of the interaction or interdependency between ontology design and functionality. And “design” could reach as far up the chain of representation as “why Description Logics and not another flavor of logic?” The term “Realism” plays a role. About five years ago there was a fairly spirited debate on this topic, reviewed here. We are reading one paper from the longer list.
Lord, P. & R. Stevens. 2010. Adding a little reality to building ontologies for biology. PLoS ONE 5(9): e12258. Available on-line here.