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This paper presents a Knowledge Base System (KBS) as a key component of a federated simulation framework which allows the investigation of (inter)dependencies among Critical Infrastructures (CIs). The KBS supports the federated simulation framework by using the ontological formalism to represent specific CI domains and their dependencies. The main advantage of the proposed ontological formalism consists on the abstraction of the description from the technological (i.e. simulation) level: the scenario can be described with a formalism used by the experts of the various CI domains. The proposed approach has been validated on a realistic scenario with actual data derived from the Rome city area. This scenario has been then used as testbed for a federated distributed simulation.