The development of biotechnology and the completion of the Human Genome Project have led to the rapid emergence of enormous amounts of genomic information. Computational resources are needed to enable researchers and clinicians to obtain quick, up-to-date information in targeted areas. The creation of this type of subject-specific knowledge base requires expertise in diverse fields. This chapter is meant to provide a detailed overview and blueprint for how to construct a cardiac-specific knowledge base like the Human Cardiac Gene Expression Knowledge Base (CaGE) (1). We have provided an overview of some of the ways to capture, organize, and store the necessary data using Perl scripts. Each group or individual interested in developing a cardiac or gene expression knowledge base will have unique needs. We hope that this information will serve as a guide for the development of new computational tools.