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.
J. Hereth, G. Stumme, R. Wille, и U. Wille. Conceptual Structures: Logical, Linguistic, and Computational Issues. Proc. ICCS '00, том 1867 из LNAI, стр. 421-437. Heidelberg, Springer, (2000)