Today, enterprises are typically in a constant process of acquiring and updating its information technologies, however typically without an overall view of the global inter and intra enterprise’s system integration. Foreseeing the future of internet, researchers have been proposing new methodologies and platforms to assist such integration in the network of applications and data. However, implementing new technologies in organizations is a difficult task, since its quality needs for architectures development are more exigent and critical than ever, due to the systems complexity and dimension, semantic needs, and to the interoperability requirements to interact with third party applications and infrastructures. Scientific foundations for EI are envisaged to roadmap such general knowledge covering the general laws of the operation on enterprise interoperability in the future of internet. This paper reports research results from ongoing European Commission supported projects that are members of the Future Internet Enterprise Systems (FInES) European Cluster. The paper draws concepts from the complex systems science and proposes a methodology for seamless networked Supply Chain Planning (SCP), by using a domain reference ontology, data model representation standards, software components evaluation and interoperability checking processes. The methodology VALTE is used to assure that enterprises use tools for SCP compliant to semantics, represented in a common reference ontology, created by the MENTOR methodology. These two horizontal methodologies are vertically supported by interoperability checking processes, which contribute for an interoperable supply chain planning system on the future internet.