Physicians nowadays have to consider a diverse range of data sources when treating a patient. Semantic clinical data warehouses allow to easily add new data and to pro-actively help the physician making sense of the data. In this work-in-progress paper we investigate an approach of using Linked Data as the access mechanism and a graph database for storage and query processing. We describe lessons learned from a case study of discovering similar genes where we use an existing similarity metric to derive new information, the Gene Ontology as a data source, and SAP HANA as an efficient graph database.