I have a similar question and was wondering if this could be solved. Basically I annotate my sequences with PANTHER13, retrieve GO annotations associated with Panther families and sub-families, and this is what I input to topGO using readMappings(). It seems to be ok, the analyses run fine, no errors, and the results seem to make sense so far. However, you would like to make a try with an ontology that is provided by Panther itself http://data.pantherdb.org/PANTHER13/ontology/PANTHERGOslim.obo.
Is there any way to do that? Basically I think that my question is the same than the one posted above, but as the number of downloads/users have bumped up since Xin's question, I decided to ask it again.
Many thanks !