The January 2006 issue of Nature Biotechnology contains four letters to the editor which reply to the infamous Are the current ontologies in biology good ontologies? article by Larisa Soldatova and Ross King. This was first blogged by nodalpointer Greg in his post The biological ontology backlash.
The first letter by Mark A. Musen, Suzanna Lewis and Barry Smith points out that finding problems in virtually any ontology is a trivial exercise and argue that the suggested approach of using SUMO, the Suggested Upper Merged Ontology, is misguided. They also acknowledge the fact that empirical evaluation of both ontology content and structure are urgently required.
The second letter, from the MGED ontology crowd including Christian Stoeckert et al argue that its not possible or appropriate to ditch the MGED ontology because of the necessity of maintaining a stable real-world resource that is widely applied in software implementations.
The third letter by Mark Miller and Rami Rifaieh of San Diego Super Duper Computer Center argue that you can't criticise all ontologies in biology by criticising one, and that the original piece should have been titled Is MGED a good ontology? rather than Are the current ontologies in biology good ontologies?
Finally, to round it all off, Larisa Soldatova and Ross King respond in the final letter. They explain where they agree and disagree with the above, standing by some but not all, of their original claims.
