The exact status is a bit complicated. MeGO indeed contains terms to fit in GO and SO (that's why I keep the SO section in MeGO) and not in any of those (as "phage" and children since they contain both genes and proteins!). I also keep a list of ACLAME functions for other "things" that do not fit in GO or SO, mostly to help me keeping track on some features that I cannot enter in GO and for other people using the DB and who like to see protein families etc. In MeGO there are links to SO and GO when the term is in one of these ontologies. I just noticed that the SO links are no active, something we need to fix.
I am in contact with both GO and SO to try to harmonize the whole thing but it is slow, mostly because of my side! Normally, Jane Lomax at GO will start a discussion on virus terms in GO next spring. The situation is quite complicated because they already have herpes virus terms in GO, organized in a way they are not satisfied with. Combining those definitions with those in PhiGO is not obvious because they are almost the same but not exactly... due to differences in host cell stuctures etc... and of course there are lots of new terms related to other eukarotic viruses that need to be added in GO and which again will have to be harmonized with phage terms.
Any link you think may be useful to MeGO from E.coliHub is welcome for us. It is my hope that people will start using this ontology to annotate phage and plasmid genes so that there is wider input into it. A plasmid annotation platform should soon be up running, for which I hope we shall contribute with MeGO. Have a nice day. Best regards. Ariane.