Found a very interesting quote:
"Both OWL-DL and function-free Horn rules are decidable fragments of first-order logic with interesting, yet orthogonal expressive power"
"Horn rules", is what prolog builds upon (a prolog statement are horn rules, AFAIS), so maybe Prolog fits into the category of "function-free horn rules"? (Gotta try to figure that out), and OWL-DL is the W3C standard for expressive semantics, that reasoners like pellet (which is available in bioclipse build upon.
The authors of the relevant paper goes on to say:
"A combination of OWL-DL and rules is desirable for the Semantic Web; however, it might easily lead to the undecidability of interesting reasoning problems. Here, we present a decidable such combination ..."
Interesting! Could this mean that a combination of Prolog and Pellet in Bioclipse can in fact be useful? Or will the SWRL support of Pellet be the preferred way to go, for joining OWL-DL with rules? Hope to know more soon.