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.
S. Chakrabarti, M. Joshi, K. Punera, and D. Pennock. WWW '02: Proceedings of the 11th international conference on World Wide Web, page 251--262. New York, NY, USA, ACM Press, (2002)