This paper addresses the problem of low impact of smart city applications observed in the fields of energy and transport, which constitute high-priority domains for the development of smart cities. However, these are not the only fields where the impact of smart cities has been limited. The paper provides an explanation for the low impact of various individual applications of smart cities and discusses ways of improving their effectiveness. We argue that the impact of applications depends primarily on their ontology, and secondarily on smart technology and programming features. Consequently, we start by creating an overall ontology for the smart city, defining the building blocks of this ontology with respect to the most cited definitions of smart cities, and structuring this ontology with the Protégé 5.0 editor, defining entities, class hierarchy, object properties, and data type properties. We then analyze how the ontologies of a sample of smart city applications fit into the overall Smart City Ontology, the consistency between digital spaces, knowledge processes, city domains targeted by the applications, and the types of innovation that determine their impact. In conclusion, we underline the relationships between innovation and ontology, and discuss how we can improve the effectiveness of smart city applications, combining expert and user-driven ontology design with the integration and or-chestration of applications over platforms and larger city entities such as neighborhoods, districts, clusters, and sectors of city activities.