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Identifying dynamical systems from experimental data is a notably difficult task. Prior knowledge generally helps, but the extent of this knowledge varies with the application, and customized models are often needed. Neural ordinary differential equations can be written as a flexible framework for system identification and can incorporate a broad spectrum of physical insight, giving physical interpretability to the resulting latent space. In the case of partial observations, however, the data points cannot directly be mapped to the latent state of the ODE. Hence, we propose to design recognition models, in particular inspired by nonlinear observer theory, to link the partial observations to the latent state. We demonstrate the performance of the proposed approach on numerical simulations and on an experimental dataset from a robotic exoskeleton.