Accessing and integrating data and knowledge for biomedical research.

OBJECTIVES: To review the issues that have arisen with the advent of translational research in terms of integration of data and knowledge, and survey current efforts to address these issues.

METHODS: Using examples form the biomedical literature, we identified new trends in biomedical research and their impact on bioinformatics. We analyzed the requirements for effective knowledge repositories and studied issues in the integration of biomedical knowledge.

RESULTS: New diagnostic and therapeutic approaches based on gene expression patterns have brought about new issues in the statistical analysis of data, and new workflows are needed are needed to support translational research. Interoperable data repositories based on standard annotations, infrastructures and services are needed to support the pooling and meta-analysis of data, as well as their comparison to earlier experiments. High-quality, integrated ontologies and knowledge bases serve as a source of prior knowledge used in combination with traditional data mining techniques and contribute to the development of more effective data analysis strategies.

CONCLUSION: As biomedical research evolves from traditional clinical and biological investigations towards omics sciences and translational research, specific needs have emerged, including integrating data collected in research studies with patient clinical data, linking omics knowledge with medical knowledge, modeling the molecular basis of diseases, and developing tools that support in-depth analysis of research data. As such, translational research illustrates the need to bridge the gap between bioinformatics and medical informatics, and opens new avenues for biomedical informatics research.