•The paper describes the information system and interoperability related challenges, trends and issues that must be addressed to support a new generation of scientific-based and technological solutions for facilitating the collaboration of existing enterprise systems.•This paper presents general research priorities and directions of related to context-aware systems, semantic interoperability, cyber-physical systems, cloud-based systems and interoperability assessment.•The listed properties are used to propose the generic abstract architecture of the Next Generation Enterprise Information Systems. The rapid changes in today's socio-economic and technological environment in which the enterprises operate necessitate the identification of new requirements that address both theoretical and practical aspects of the Enterprise Information Systems (EIS). Such an evolving environment contributes to both the process and the system complexity which cannot be handled by the traditional architectures. The constant pressure of requirements for more data, more collaboration and more flexibility motivates us to discuss about the concept of Next Generation EIS (NG EIS) which is federated, omnipresent, model-driven, open, reconfigurable and aware. All these properties imply that the future enterprise system is inherently interoperable. This position paper presents the discussion that spans several research challenges of future interoperable enterprise systems, specialized from the existing general research priorities and directions of IFAC Technical Committee 5.3,11IFAC Technical Committee 5.3 « Enterprise Integration and Networking », http://www.ifac-tc53.org namely: context-aware systems, semantic interoperability, cyber-physical systems, cloud-based systems and interoperability assessment.