We present the method developed for migrating the Foundational Model of Anatomy (FMA) from its representation with frames in Protégé to its logical representation in OWL and our experience in reasoning with it. Despite the extensive use of metaclasses in Protégé, it proved possible to convert the FMA from Protégé into OWL DL, while capturing most of its original features. The conversion relies on a set of translation and enrichment rules implemented with flexible options. Unsurprisingly, reasoning with the FMA in OWL proved to be a real challenge, due to its sheer size and complexity, and raised significant inference problems in terms of time and memory requirements. However, various smaller versions have been successfully handled by Racer. Some inconsistencies were identified and several classes reclassified. The results obtained so far show the advantage of OWL DL over frames and, more generally, the usefulness of DLs reasoners for building and maintaining the large-scale biomedical ontologies of the future Semantic Web.