On the topic of foundational ontologies that are useful for the biomedical domain, I feel urged to refer to the DOLCE foundational ontology:
http://www.loa-cnr.it/DOLCE.html DOLCE lite is available as a modularized OWL ontology. The OWL version of DOLCE is already quite established and stable. The BFO SNAP/SPAN ontology and the relations ontology are almost totally redundant with the basic modules of DOLCE. The only innovations of BFO might be the two "transformed" and "derives-from" properties, but these can also be added to DOLCE. BFO also does not seem to offer any remedies to the shortcomings that DOLCE is suffering from (especially the problems one runs into when trying to express temporal indexing over properties like part-of). As DOLCE is more extensive and has been very stable for some time, while the OWL version of BFO is still under creation, I don't think that there are any arguments for choosing BFO over DOLCE, at least at the time. Fortunately, the redundandy between both ontologies should make it easy to align them and settle this 'conflict' peacefully. kind regards, Matthias Samwald
