The rapid expansion of the Internet of Things (IoT) will generate a diverse range of data types that needs to be handled, processed and stored. This paper aims to create a multi-agent system that suits the needs introduced by the IoT expansion, thus being able to oversee the Big Data collection and processing and also to maintain the semantic links between the data sources and data consumers. In order to build a complex agent oriented architecture, we have assessed the existing agent oriented methodologies searching for the best solution that is not bound to a specific programming language of framework, and it is flexible enough to be applied in such a divers domain like IoT. As complex scenario, the proposed approach has been applied to medical diagnosis and motoring of mental disorders.