Security is one of the most challenging requirements to construct and develop smart cities. That is due to fact that smart city utilizes IoT advanced solutions to provide the integration of the numerous, and heterogeneous smart devices. The heterogeneity of IoT creates the opportunity to launch multiple cyberattacks against different smart city services. Thus, security have been considered as a major issue in smart city development and research. In this survey, we provide an overview of the research works that have investigated security in smart city from different aspects. We demonstrate researches that have explored security of smart city from general perspective. Then, we introduce an overview of the use of machine learning to secure smart cities. Finally, we present the development of ontologies for security purposes, from general perspective and for smart city in particular. We highlight the most significant observations on the presented research works which need to be considered in future to enhance security in IoT-based smart city.