I am using the script go2fmt.pl to convert obo file to go format.
There seem to be a problem with the obsolete terms relationships.
Problem with obsolete terms seem to also occur using the Java
DAG-Edit script obo2flat (but the problem is slightly different and I
guess this is for another bug report).
The obsolete terms are not being assigned relationships to the
appropriate obsolete aspect.
I tested loading the converted scripts to AmiGO.
This is when loading the OBO file - which is the way it's supposed to
This is when loading the GO format files after conversion:
Please let me know if you need examples of files - or db dumps.