The objectives of this paper are (a) to motivate the adoption of semantic graphical models of threat relations and countermeasures in the design and operation of cyber-physical systems (CPS), and (b) to raise awareness of the various benefits which systems security engineers (SSEs) stand to gain by adopting such practices. Specifically, we propose that a Semantic Threat Analysis (STA) can endow SSEs with a comprehensive, extensible, machine-readable, and logically inferable model of system features. An STA shaped to the specific architecture and security requirements of a CPS environment can support the identification and visualization of system interdependencies and process flows among network, computing, mechanical, security, and access control components. The proposed STA process presupposes a team-oriented systems engineering approach employing a combination of subject matter experts (SMEs) and ontologists who can bring their respective expertise together to bear on the task.