The integration of heterogeneous biomedical information is one important step towards providing the level of personalization required in the next generation of healthcare provision. In order to provide the computer-based decision support systems needed to access this integrated healthcare information it will be necessary to handle the semantics of (amongst other things) medical protocols. The EC FP6 Health-e-Child project aims to develop an integrated healthcare platform for European paediatrics and decision support tools to access personalized health information. This paper introduces both the integrated data model in the Health-e-Child project and through a case study using the brain tumour protocols it demonstrates the semantic annotation of patient data acquired in the project using UMLS as the primary source of semantic data.