Run GO rule 20 (obsolete term repair) before GO rule 28 (term aspect check)
dustine32 opened this issue · 2 comments
Originating from geneontology/pipeline#242 (comment).
Use case here is converting a GPAD, which lacks aspect column, into GAF. For most annotations the null aspect is correctly filled in from the ontology term property hasOBONamespace
. But this property is missing for obsolete terms (like GO:0044212), so the resulting GAF line will have a blank aspect column. To fix:
we want to aim to repair the obsoleted term (via GO rule 20) before attempting to extract the aspect in GO rule 28. This way the correct term (GO:0000976) is in place for aspect extraction.
So far, this reordering of rules just looks to involve moving up a few code lines in gpadparser.py. We may want to also do this in gafparser.py
for consistency even though it's likely a non-issue for GAF inputs since the aspects are already explicitly set?
@dustine32 I guess this was a problem for geneontology/pipeline#242 , right?
Just to keep everybody at the same place, we can bump go-site master
to 2.7.6
for ontobio and then have the test branches catch up there.
updated ZFIN branch and rerunning.