Agents producing and exchanging knowledge are forming as a whole a socio-semantic complex system, whose study offers theoretical challenges, with the perspective of solving a reconstruction problem in social sciences, as well as practical challenges, with potential applications enabling agents to know the dynamics of the system they are participating in. We show that several significant aspects of the structure of a knowledge community are primarily produced by the co-evolution between agents and concepts, i.e. the evolution of an epistemic network. We rebuild taxonomies of knowledge communities from low-level observation of relationships between agents and concepts, using Galois lattices; achieving ultimately an historical description (inter alia field progress, decline, specialization, interaction). We then micro-found various stylized facts regarding this particular structure by exhibiting processes at the level of agents accounting for the emergence and morphogenesis of epistemic community structure, assuming that agents and concepts are co-evolving.