The design and implementation of agro-ecology IoT applications is a non-trivial task since the data processed in such applications are typically complex and heterogeneous. Moreover, these applications are implemented using different systems and technologies, over complex IoT communication network layers (edge, fog, cloud). The existing system design methods fail to effectively represent data in such a scenario. In this position paper we report and discuss the open issues for a new, dedicated design method, based on our initial experience in implementing an agro-ecology IoT system.