Just came across the GO-friends mailing list:
As previously announced, The Gene Ontology Consortium has now introduced three new relationship types
– regulates,negatively_regulates and positively_regulates — into the Biological Process ontology. These relationship types improve the representation of regulatory processes in the GO.
Please see the following pages on the GO website for more information:
The new relationship types will be visible through the AmiGO browser by the end of this month and at the various model organism databases that display GO as they update their ontology files.
on behalf of the GO Consortium
Keep this in mind as you use GO tools–some tools will implement the changes before others, and it may affect what you see in different databases.
Congrats to the GO team, I’m sure it was a major project to wrangle.