The Health Data Ontology Trunk (HDOT). Towards an ontological representation of cancer-related knowledge

Ontologies play a central role in new IT strategies for personalized medicine that enhance the communication between patients and health care providers. In this paper we present the Heath Data Ontology Trunk (HDOT) and how it is used for this purpose within the p-medicine project. We describe crucial methods in its development, in particular its modularity. The main benefit of a domain middle-layer ontology approach is that the latter can be further extended and specialized in different but interrelated modules according to more specific biomedical and clinical needs and requirements within the same semantic framework. As an example of a modular extension of HDOT relevant to cancer research and treatment we describe a first prototype of the HDOT pathological formation module. We demonstrate the usefulness of this module in two scenarios: the semantic integration of heterogeneous biobank metadata and the design and administration of Case Report Forms (CRFs).