What the Alliance is about is to try and achieve a uniform data structure that makes it possible to establish, with different levels of certainty, relationships between concepts in a given domain (we start with biomedical). The idea of a single, overarching, monolithic ontology doesn’t fit this model. Instead, several ontologies must co-exist, and yes, if combined, they can yield contradictions.
O. Medelyan, and I. Witten. JCDL '06: Proceedings of the 6th ACM/IEEE-CS joint conference on Digital libraries, page 296--297. New York, NY, USA, ACM, (2006)