Enabling system-wide capabilities is a key aspiration of systems engineering. It comes as no surprise then that a number of system modeling techniques have turned their attention to the analysis and design of capabilities. Despite that, these tasks have remained challenging due to the interactive and emergent nature of capabilities, as evidenced by the cases of agility, resilience, adaptability and security. Modeling capabilities requires a proper understanding of capability-related concepts and also how capabilities interact and emerge. To address these challenges, this paper proposes a capability reference ontology (Creon) grounded in system science, emergence explanations, and disposition theories. The ontology aims to enhance the modeling of emergent capabilities and capability relationships in systems engineering. By leveraging concepts from the Unified Foundational Ontology (UFO), Creon supports a comprehensive representation of capabilities. We illustrate the use of the ontology in a transportation context, and present some implications for system capability modeling.