GPAD writer might be dropping qualifiers when NOT is used

[dustine32]

Not sure if this problem is restricted to the GO pipeline but the product is where I observed it: http://current.geneontology.org/annotations/mgi.gpad.gz

It's also in the wb.gpad. I think something's up with the GPAD parsing/writing NOT qualifiers in ontobio that's affecting the release GPADs. Here's an example NOT from the upstream MGI GPAD:

MGI     MGI:1919025     NOT|enables     GO:0005506      MGI:MGI:3815273|PMID:18712936   ECO:0000314                     20110412        MGI

and here's the GO release GPAD:

MGI     MGI:1919025     NOT|    GO:0005506      MGI:MGI:3815273|PMID:18712936   ECO:0000314                     20110412          MGI

It looks like the enables qualifier is getting dropped.

As a fun anomaly, this NOT line isn't dropping the other qualifier colocalizes_with in the release GPAD:

MGI     MGI:1316648     NOT|colocalizes_with    GO:0030315      MGI:MGI:4838689|PMID:20833135   ECO:0000314        20131111        UniProt part_of(EMAPA:32716)

Tagging @dougli1sqrd