With increasingly detailed physics questions to ask, and with more advanced diagnostics available, there is a strong case for trying to generalise the way analysis of diagnostic data, and connection to underlying physics models, is done in today's experiments. With current analysis chains, it is difficult, verging on impossible, to fully grasp the exact assumptions, hidden in different legacy codes, that goes into a full analysis of the main physics parameters in an experiment. We show that by using Bayesian probability theory as the underlying inference method, it is possible to generalise scientific analysis itself, and therefore build an effective and modular scientific inference software infrastructure. The Minerva framework uses the concept of Bayesian graphical models to model the full set of dependencies, functional and probabilistic, between physics assumptions and diagnostic raw data. Using a graph structure, large scale inference systems can be modularly built that optimally and automatically use data from multiple sensors. The framework, used at the JET, MAST, H1 and W7-X experiments, is exemplified by a number of JET applications, ranging from inference on the flux surface topology to profile inversions from multiple diagnostic systems.'