Due to its computing power and storage capacity, the Cloud has been integrated with Cyber-physical systems, thus creating complex and powerful Cyber-physical Cloud platforms. It is important that these systems have proper security and clear specifications in order to be trustworthy and reliable. To address these requirements and issues we propose a semantic, ontology-based architecture for Cyber-physical Cloud systems. It is based on Semantic Sensor Network Ontology and STAC (Security Toolbox: Attacks & Countermeasures) Ontology, aggregating domains and clusters of sensing nodes with a central backbone which processes data and stores it in the Cloud, taking into account also the security properties of such a complex system.