This paper presents an ontological self-organizing map (OSOM), which is used to produce visualization and functional summarization information about gene products using gene ontology (GO) similarity measures. The OSOM is an extension of the self-organizing map as initially developed by Kohonen, which trains on data composed of sets of terms. Term-based similarity measures are used as a distance metric as well as in the update of the OSOM training procedure. We present an OSOM-based visualization method that shows the cluster tendency of the gene products. Also demonstrated is an OSOM-based functional summarization which produces the most representative term(s) (MRT) from the GO for each OSOM prototype and, subsequently, each gene product cluster. We validated the results of our method by applying the OSOM to a well-studied set of gene products.