Question Answering websites are popular repositories of expert knowledge and cover areas as diverse as linguistics, computer science, or mathematics. Knowledge is commonly organized via user defined tags which implicitly create population folksonomies. However, the interplay between latent knowledge structures and the answering behavior of users has not been fully explored yet. Here, we propose a model of a dynamical tagging process guided by taxonomies, devise a robust algorithm that allow us to uncover hidden topic hierarchies, apply our method to analyze several Stack Exchange websites. Our results show that the dynamics of the system strongly correlate with uncovered taxonomies.