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In this paper, we discuss the use of the Systems science, starting from the General Systems Theory, for Enterprise Interoperability (EI). We review and discuss main systemic concepts, highlighting the system properties that are important for interoperability and solutions to deal with related issues at a systemic level. We then propose an ontology, which grounds the existing Framework for Enterprise Interoperability (CEN/ISO 11354) within a systemic model. This ontology constitutes a basis for modelling of systems, barriers and solutions related to EI that might be exploited in a systemic enterprise modelling process for diagnosis or decision-aid in establishing interoperability.