Genome studies have revolutionised cancer research in recent years as high-throughput technologies can now be used to identify sets of genes potentially related with different processes in cancer. However, managing all this data and organising it into useful datasets is still a challenge in the bioinformatics field. Finding relationships between the molecular and genomic information and the clinical information available, within the medical informatics domain, is currently driving the development of translational research in biomedicine. The dispersion and complexity of the molecular information, the poor adherence to standards, together with the fast evolution of the experimental techniques, pose obvious challenges for the development of integrated molecular resources. In parallel, restricted access to medical information together with the gaps in the development of standard terminologies are typical limitations in the area of medical informatics. The development of research projects combining medical and molecular information together with the current efforts to standardise and integrate databases and terminologies are described in this review as a demonstration of the fruitful activity in this area.