[Pombase-chado] [ pombase-Chado-3590723 ] 'from=' data missing from GAF for IC

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Chado item #3590723, was opened at 2012-11-28 08:01
Message generated for change (Comment added) made by gomidori
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 7
Private: No
Submitted By: Midori Harris (gomidori)
Assigned to: Kim Rutherford (kim_rutherford)
Summary: 'from=' data missing from GAF for IC

Initial Comment:
Problem! The GAFs being written out from Chado don't have anything in column 8 (with/from) where the evidence (col 7) is IC.

I used pombase-build-2012-11-25-v2-l1.gaf to the GAF in the GO repository. I looked a couple other GAFs from the dumps as well, and none had the data (tried pombase-build-2012-10-19-v1-l1.gaf, pombase-build-2012-11-05-v1-l1.gaf, pombase-build-2012-11-18-v2-l1.gaf).

I didn't try to chase up every annotation, but the handful I spot-checked all had the requisite data in the embl files. Just one example:

FT                   /GO="aspect=P; term=histone acetylation; GOid=GO:0016573;
FT                   evidence=IC; db_xref=GO_REF:0000001; from=GO:0035267;
FT                   date=20090301"

becomes

PomBase SPAC1F5.11c     tra2            GO:0016573      GO_REF:0000001  IC              P       NuA4 complex phosphatidylinositol pseudokinase complex subunit Tra2             protein taxon:4896      20090301        PomBase

The GO filter-gene-association.pl script is totally supposed to catch these, but equally totally failed -- it told me "Congratulations, there are no errors." and I didn't realize until today that it was lying. I'm reporting that to GO.

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>Comment By: Midori Harris (gomidori)
Date: 2012-12-02 07:36

Message:
That looks MUCH better - thanks!

I'll fix the problem lines, and sooner or later GO SVN will be back among
the living and I'll commit the new GAF ...

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Comment By: Kim Rutherford (kim_rutherford)
Date: 2012-12-02 00:21

Message:
This is fixed in the latest load:
   http://curation.pombase.org/kmr44/dumps/pombase-build-2012-11-28-v3-l1/

Sorry, the GAF writer was ignoring the froms.

The fix added the from to most of the IC annotations.  I've made a file
with the ones that look like problems: 
  Dropbox/pombase/Chado/GAF_IC_annotation_problems.txt

There's only a handful.  Some have no from, some have a from that isn't a
GO term (maybe that's OK?) and there is one IMP annotation that has a from
in Chado, but perhaps shouldn't.

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