BarleyBase is a web-accessible public data resource of Affymetrix GeneChip data for Barley and Arabidopsis that is supported by the USDA NRI program. The exponential increase in microarray gene expression data demands well-annotated public repositories to store and manage this valuable information. However, microarray gene expression profiles are highly context dependent and are sensitive to sample and processing conditions. How to accurately and efficiently represent this information are two major challenges in establishing microarray databases. These concerns are addressed by integrating the MIAME (Minimum Information About a Microarray Experiment) standards and the structured Plant Ontology into the design and implementation of BarleyBase. BarleyExpress, a web-based data submission tool to BarleyBase, allows users to input the MIAME information directly into the database and to explicitly use the Plant Ontology controlled vocabularies to annotate microarray gene expression profiles. The application of the MIAME standard and the Plant Ontology puts the experimental data in BarleyBase in a highly biological and analytical context and enables the valuable insights into the biological processes. BarleyBase also serves as a prototype for the management of microarray gene expression data for other cereal plants. BarleyBase is accessible at http://barleybase.org