For almost 2 years now, there has been a formal collaboration between the Gene Ontology Consortium and the PANTHER database (5). As a result, in PANTHER 7, all molecular function, biological process and cellular component terms are exclusively GO terms [previous versions of PANTHER used the PANTHER/X ontology (1), though a mapping file to GO was provided]. The PANTHER/X biological process ontology has been retired, but we have retained the PANTHER/X molecular function ontology and renamed it ‘Protein Class’ since many terms are quite different from those in GO, and we have gotten considerable feedback from users about its utility.
