After completion of the Human Genome Project, various post-genomics approaches are being undertaken to utilize the genome information such as for drug target discovery and personalized medicine. In Fall 2003 the U.S. National Institutes of Health announced the Roadmap, which contained new chemical genomics initiatives for screening of useful chemical compounds including imaging probes and drug leads. Our COE program was initiated before the NIH Roadmap, but we had foreseen the importance of small chemical compounds. Our program consists of three research components: pharmacogenomics for drug target discovery, chemogenomics for drug lead discovery, and environmental genomics for understanding the relationship between genomic and environmental information, especially, drug targets and drug leads, in terms of the molecular interaction networks. Searching for a lead compound and its target is just one example of searching for a perturbant, its target, and any consequence of the perturbed biological system. Therefore, our approaches currently focused on pharmaceutical science can be generalized and applied to wider areas of biological sciences. We are developing bioinformatics technologies to integrate genomic and chemical information, and to decipher molecular wiring diagrams involving both endogenous and exogenous molecules. This will enable basic understanding of the biological systems and their interactions with the chemical environments, as well as new medical and industrial applications.