This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function.

A prerequisite to systems biology is the integration of heterogeneous experimental data, which are stored in numerous life-science databases. However, a wide range of obstacles that relate to access, handling and integration impede the efficient use of the contents of these databases. Addressing these issues will not only be essential for progress in systems biology, it will also be crucial for sustaining the more traditional uses of life-science databases.

SEMEDA is available at http://www-bm.ipk-gatersleben.de/semeda/. Database providers who intend to grant access to their databases via SEMEDA are encouraged to contact the authors.

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