BarleyExpress is a web-based microarray experiment data submission tool for BarleyBase, a public data resource of Affymetrix GeneChip data for plants. BarleyExpress uses the Plant Ontology vocabularies and enhances the MIAME guidelines to standardize the annotation of microarray gene expression experiments. In addition, BarleyExpress provides explicit support for factorial experiment design and template loading methods to ease the submission process for large experiments.