Workflow for conducting controlled gene set enrichment experiment using the GOA database. 1) PubMed citations are identified that are linked to genes in the context of GOA annotations. 2) The title and abstracts of each of these articles are mined for GO terms using the Annotator. 3) The mined terms are assigned as candidate annotations to the genes linked to the relevant PubMed citations. 4) For each GO term a) create a "true positive" gene set based on the annotations for that term from GOA, b) compare this gene set to the gene set produced for that GO term by the PubMed mining process, c) expand the PubMed-mined annotation set with the annotations mined from the Gene Wiki and repeat the comparison to the GOA-derived gene set. Compare the results from steps 4b and 4c to quantify the impact that the Gene Wiki-derived annotations have on gene set enrichment analysis where the 'correct' set is predetermined.