Systems of systems (SoS) are dynamic coalitions of distributed, autonomous and heterogeneous systems that collaborate to achieve a common goal. While offering several advantages in terms of scalability and flexibility, the SoS paradigm has a strong impact on systems interoperability and on the security requirements of the collaborating parties. In this paper, we introduce a service-oriented security framework that protects the information exchanged among the parties in an SoS, while preserving parties' autonomy and interoperability. Confidentiality and integrity of information are protected by combining context-aware access control with trust management. Autonomy and interoperability among parties are enabled by the use of ontology-based services. More precisely, parties may refer to different ontologies to define the semantics of the terms used in their security policies and to describe domain knowledge and context information; a semantic alignment technique is then employed to map concepts from different ontologies and align the parties' vocabularies. We demonstrate the applicability of our solution by deploying a prototype implementation of the framework in an SoS in the maritime safety and security domain.