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In this paper we propose KOIOS++, which automatically processes natural language queries provided by handwritten input. The system integrates several recent achievements in the area of handwriting recognition, natural language processing, information retrieval, and human computer interaction. It uses a knowledge base described by the resource description framework (RDF). Our generic approach first generates a lexicon as background information for the handwritten text recognition. After recognizing a handwritten query, several output hypotheses are sent to a natural language processing system in order to generate a structured query (SPARQL query). Subsequently, the query is applied to the given knowledge base and a result graph visualizes the retrieved information. At all stages, the user can easily adjust the intermediate results if there is any undesired outcome. The system is implemented as a web-service and therefore works for handwritten input on digital paper as well as on input on Pen-enabled interactive surfaces. Furthermore, we build on the generic RDF-representation of semantic knowledge which is also used by the linked open data (LOD) initiative. As such, our system works well in various scenarios. We have implemented prototypes for querying company knowledge bases, the DBPedia1, the DBLP computer science bibliography2, and a knowledge base of the DAS 2012.