Building shared and reusable ontologies, both in an operational and more conceptual sense, needs precise definition of system of interest, classification of its relations by means of topological analysis, and explanation of the concepts through mereological tools (for example decomposition of an object in its parts, or a class in its subclasses). Our work presents an attempt to apply these procedures to urban systems, beginning from the corpus of theories developed in urban system analysis to achieve an ontology of the city with the already mentioned suitable features, underlining in particular three levels (physical, socio-economical, and mental level) through which it’s possible to observe the city.