As a subproject, I'm now focusing on doing some comparison between reasoning in Prolog and Pellet, using example data from NMRShiftDB.org. Below I'm documenting my planning, + any new findings while I'm digging in to this subpeoject.
I Just read this paper on using thea for OWL (Web Ontology Language) reasoning from within Prolog.
Pellet, the reasoning system already integrated in Bioclipse, is based on so called "Description Logics".