Data that has been collected in the course of clinical trials are potentially valuable for additional scientific research questions in so called secondary use scenarios. This is of particular importance in rare disease areas like paediatric oncology. If data from several research projects need to be connected, so called Core Datasets can be used to define which information needs to be extracted from every involved source system. In this work, the utility of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) as a format for Core Datasets was evaluated and a web tool was developed which received Source ODM XML files and–via Extensible Stylesheet Language Transformation (XSLT)–generated standardized Core Dataset ODM XML files. Using this tool, data from different source systems were extracted and pooled for joined analysis in a proof-of-concept study, facilitating both, basic syntactic and semantic interoperability.