The growth of the Internet of Things (IoT) results in a proliferation of different protocols (ZigBee, Bluetooth, 6LowPAN, Z-Wave, Wi-Fi, etc.). Organizations tend to quickly deploy several IoT applications over time and thus face heterogeneous IoT systems, combining different IoT protocols in different places of the overall system. This heterogeneity of protocols makes these networks hard to monitor or control, and some misconfigurations or unexpected device behaviours may even expose users to security issues. In this work, we propose the IoTMap system. IoTMap models interconnected and heterogeneous IoT networks, combining different protocols, by providing a generic stack and a unified packet format. IoTMap builds an iterative graph model where high-level semantics can progressively be deduced, ranging from packet transmission to application-type analysis. As such, IoTMap detects application behaviours amongst devices implementing different protocols, interconnected through a multi-protocol hub. In its current implementation (available at https://github.com/AlgoSecure/iotmap), IoTMap can inspect Zig- Bee, BLE and 6LowPAN networks.