Had a few discussions in the lab today where we required an ontology or set of Gene Ontology terms to describe a protein complex rather than its constituents. I've seen ontologies for constituent parts of the cell but not for more transient complexes. In part the need for this should be guided by the likes of the systems biology graphical notation framework where the idea of units of activity come together to form distinct activities in cooperation. However, I have still haven't seen an actual ontology of protein complexes.