The Ontology Summit 2012 explored the current and potential uses of ontology, its methods and paradigms, in big systems and big data: How ontology can be used to design, develop, and operate such systems. The systems addressed were not just software systems, although software systems are typically core and necessary components, but more complex systems that include multiple kinds and levels of human and community interaction with physical-software systems, systems of systems, and the socio-technical environments for those systems which can include cultural, legal, and economic components. The focus themes used for this exploration were Big Systems Engineering, Big Data Challenge, Large Scale Domain Applications, and cross-cutting aspects Ontology Quality, and Federation and Integration of Systems.The Ontology Summit 2012 consisted of over three months of intensive virtual collaborative elaboration of these issues in presentations, panels, and group email. The culmination of these activities was a face-to-face Symposium at the US National Institute of Standards and Technology NIST, Gaithersburg, MD, USA, 12--13 April 2012. The primary product of this Ontology Summit is the communique reported here. But there are other products, some continuing as collaborative, more specifically focused analysis and modeling efforts aligned with various open standards activities.Behind all of these particular products, of course, is the real overriding purpose of the Ontology Summit 2012, which was: the joint collaboration of three distinct communities, the ontology, systems engineering and big systems stakeholder communities, who came together to address common problems, create common understanding and propose common solutions.