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In this paper we propose a method for efficient management of large spatial ontologies. Current spatial ontologies are usually represented using an ontology language, such as OWL and stored as OWL files. However, we have observed some shortcomings using this approach especially in the efficiency of spatial query processing. This fact motivated the development of a hybrid approach that uses an R-tree as a spatial index structure. In this way we are able to support efficient query processing over large spatial ontologies, maintaining the benefits of ontological reasoning. We present a case study for emergency teams during Search and Rescue (SaR) operations showing how an Ontology Data Service (SHARE-ODS) can benefit from a spatial index. Performance evaluation shows the superiority of our proposed technique compared to the original approach. To the best of our knowledge, this is the first attempt to address the problem of efficient management of large spatial ontology bases.