Cyber physical systems (CPS) are an integration of computational and physical processes, where the cyber components monitor and control physical processes. Cyber-attacks largely target the cyber components with the intention of disrupting the functionality of the components in the physical domain. This dissertation explores the role of semantic inference in understanding such attacks and building resilient CPS systems. To that end, we present SIMON, an ontological design and verification framework that captures the intricate relationship(s) between cyber and physical components in CPS by leveraging several standard ontologies and extending the NIST CPS framework for the purpose of eliciting trustworthy requirements, assigning responsibilities and roles to CPS functionalities, and validating that the trustworthy requirements are met by the designed system. We demonstrate the capabilities of SIMON using two case studies – a vehicle to infrastructure (V2I) safety application and an additive manufacturing (AM) printer. In addition, we also present a taxonomy to capture threat feeds specific to the AM domain.