International audienceEmergence and complex systems have been the topic of many papers and are still disputed concepts in many fields. This lack of consensus hinders the use of these concepts in practice, particularly in modelling. All definitions of emergence imply the existence of a hierarchical system: a system that can be observed, 15 measured and analysed at both macroscopic and microscopic levels. We argue that such systems are well described by mathematical graphs and, using graph theory, we propose an ontology (i.e. a set of consistent, formal concept definitions) of dynamic hierarchical systems capable of displaying emergence. Using graph theory enables formal definitions of system macro-state, micro-state and dynamic structural ch...