Gene Logic is using microarrays (including the Affymetrix GeneChip™) to construct a comprehensive gene expression database for pharmaceutical, biotech and academic users. We are determining thousands of expression profiles of normal and diseased mammalian tissues, experimentally manipulated animals and cell lines, and tissues and cells treated with pharmacologic and toxic doses of a diversity of compounds. The technical issues in generating this data as well as the complex challenges of storing, analysing and integrating it with public data will be presented. In addition, the biological relevance of data generated from this approach will be demonstrated as an example of the type of functional information that can be derived and applied to pharmaceutical and diagnostic research and development.