Editing in OE and seeing inferences in Protege:

# open ubiq-ligase-complex.obo in OBO-Edit 2.1.1beta4 or higher
# Save as OWL (use the same filename with the .owl suffix)
# open ubiq-ligase-complex.owl in Protege4
# turn on reasoning in P4
# Navigate to 'ubiquitin ligase complex' in OE
# Add a subclass of 'ubiquitin ligase complex' called 'cytoplasmic ubiquitin ligase complex'
 # NOTE:: do this *directly* under the 'ubiquitin ligase complex' class, don't move things around!
 # NOTE: this class already exists in the main GO, but it has been removed for this tutorial example
# Give it a logical definition (genus-differentia)
# Save the OWL
# Protege should prompt you to load the new OWL
# Find your new class in Protege
# do the same steps for 'nuclear ubiquitin ligase complex'

Next: editing in Protege

# Find your two new classes and give them textual definitions
# Save the OWL
# OE should prompt you that the OWL has changed
# Examine the definitions in OE
# Make minor modifications - e.g. adding "." after end of definition
# Save and examine in P4