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As society moves toward greater interconnectedness, the complexity and interdependence of systems-of-systems (SoSs) increase, giving rise to multifaceted safety hazards and security threats. The critical need for effective hazard and threat analysis within SoSs is addressed in this licentiate thesis by focusing on the development and application of specialized ontologies. The interconnected nature of safety and security is highlighted, and a novel ontological framework that integrates these aspects into a unified analysis tool is proposed. The research was organized around five main contributions:

- The application of a Hazard Ontology (HO) to a cyber-physical SoS at a quarry site equipped with autonomous vehicles, enabling the identification of hazard sources, causes, and consequences.

- Through a systematic literature review of security ontologies, essential security concepts and their relationships were identified. These concepts were harmonized with established security standards, such as NIST SP 800-160 and ISO/IEC 27001.

- The development of a Combined Security Ontology (CSO), based on the Unified Foundational Ontology (UFO), by synthesizing security concepts derived from the literature review and mapping them to a foundational safety ontology to bridge the gap between the security and safety domains.

- A comparative analysis of the HO and the CSO was conducted, highlighting similarities and differences in concepts and relationships, and clarifying the integration challenges and opportunities between safety and security ontologies.

- The proposed Hazard and Threat Ontology (HTO) extends the HO and integrates elements from the CSO, facilitating simultaneous analysis of hazard and threat within SoSs.

The thesis emphasizes the need for evolving ontological methods to enhance hazard and threat analyses in SoSs, ensuring their adaptability to dynamic operational environments and emerging challenges. With this integrated approach, the thesis aims to contribute to the safety and security domains within systems engineering by providing a methodological framework that is both innovative and applicable to real-world scenarios.