One of the major challenges in the post-genome era is to determine the cellular functions of genes and their products, to understand how the interactions among the entities in cellular contexts could yield a living cell. To attack this problem, Gene Expression Tool kit (GET) project was launched in Iowa State University. This thesis will describe a general model for representing metabolic and regulatory biological networks. The model is implemented in a relational database: MetNet DB. MetNet DB serves as an information hub in GET software package. The thesis will also present one of MetNet DB practical applications: Probe database, which is based on the information derived from MetNet DB. Probe database provides the integrated functional annotations for Arabidopsis microarray probes. Currently Affymetrix Arabidopsis GeneChip AtGenomel, ATHI and AFGC EST microarray, three large datasets are supported. Probe database could be seamlessly integrated to other microarray data analysis tools, such as GeneSpring. This provides an efficient annotation for mining Arabidopsis RNA profiling data.