GOclasses: molecular function as viewed by proteins

Motivation: The Gene Ontology (GO) is now the standard for describing gene and protein functions. By studying the protein function space as described by the GO, we can improve the quality of functional predictions and automated annotations and ultimately, the quality of the GO structure. Results and Conclusions: We present an approach for the large scale study of the protein function space, and propose a set of strategies to mine that space with the goal of detecting erroneous or inconsistent annotations as well as underlying relationships in the GO.