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In recent years, machine learning (ML) has been proposed to devise data-driven parametrisations of unresolved processes in dynamical numerical models. In most cases, the ML training leverages high-resolution simulations to provide a dense, noiseless target state. Our goal is to go beyond the use of high-resolution simulations and train ML-based parametrisation using direct data, in the realistic scenario of noisy and sparse observations. The algorithm proposed in this work is a two-step process. First, data assimilation (DA) techniques are applied to estimate the full state of the system from a truncated model. The unresolved part of the truncated model is viewed as a model error in the DA system. In a second step, ML is used to emulate the unresolved part, a predictor of model error given the state of the system. Finally, the ML-based parametrisation model is added to the physical core truncated model to produce a hybrid model. The DA component of the proposed method relies on an ensemble Kalman filter while the ML parametrisation is represented by a neural network. The approach is applied to the two-scale Lorenz model and to MAOOAM, a reduced-order coupled ocean-atmosphere model. We show that in both cases the hybrid model yields forecasts with better skill than the truncated model. Moreover, the attractor of the system is significantly better represented by the hybrid model than by the truncated model.