[Annotation] check for ND + additional annotation

[Midori Harris]

I think the user said there was an RCA annotation; anyway, it was S.c. 
CWC32.

m

On Thu, 4 Sep 2008, Pascale Gaudet wrote:

> Midori,
> 
> Were those ND found with IEAs or with other evidence codes?
> 
> I also wonder, what happens in cases where there is no literature but other evidence for
> annotations, such as ISS, IGC, etc, if the ND means no experimental data?
> 
> Pascale
> 
> Midori Harris wrote:
>       The reason I brought it up is that apparently not all users appreciate the
>       distinction between "no literature" and "no data of any kind". The fact that
>       we've named the code "ND" contributes a bit to that confusion. More importantly,
>       the documentation that Mike quoted says "no information", and it's perhaps not
>       surprising that the user didn't translate that to "no experimental data/no
>       literature".
>
>       While this exchange has pointed out good reasons for retaining both ND and
>       computational annotations, I do think the documentation needs to be clarified.
>
>       m
>
>       On Wed, 3 Sep 2008, Harold Drabkin wrote:
>
>             We also allow IEA along with ND as ND means no literature. Also, we
>             have triggers in our Editorial Interface that
>             1. removes ND to an aspect when a non IEA is entered.
>             2. prevents an ND being added if a non-IEA exits for the gene.
>
>             We have various qc's operating based on the ND status of a gene and
>             if new literature comes in that is indexed to the gene, etc.
>             The users need to be made more aware that the ND specifically means
>             no literature known to support higher annotations at the time.
>
>             h
>
>             Pascale Gaudet wrote:
>                   That seems to make sense. Otherwise, how do you know a
>                   curator has reviewed the literature for that gene?
>
>                   Stacia Engel wrote:
>                   > the gene in question was a yeast gene, CWC23.  there is
>                   ND to generic BP > because we have no experimental data
>                   for that gene.
>                   >
>                   > the gene has computational annotations from both
>                   UniProtKB and bioPIXIE. at > SGD, we don't remove NDs to
>                   root nodes when only computational annotations exist.
>                   >
>                   > stacia
>                   >
>                   >
>                   > On Sep 3, 2008, at 11:37 AM, Judith Blake wrote:
>                   >
>                   >> Typically, I think this should be done at the time of
>                   generating the >> annotation...even an IEA.  Each group
>                   might consider implementing something >> to QC this, but
>                   a QC at the time of submission of data file to AmiGO
>                   would be >> good too.
>                   >>
>                   >> Judy
>                   >>
>                   >>
>                   >>
>                   >> Midori Harris wrote:
>                   >>> Hi,
>                   >>>
>                   >>> We received a query on the GO Help list from a user
>                   who noticed a gene that >>> was annotated to both the
>                   biological process (BP) root with ND, and >>> annotated
>                   to a non-root BP term with another evidence code. I
>                   agreed with >>> him that it doesn't make sense to keep
>                   the ND/root annotation if a "real"
>                   >>> annotation could be made to a term in the same
>                   ontology. Would it be >>> worthwhile to add a check for
>                   cases like this, perhaps in Mike's script?
>                   >>>
>                   >>> cheers,
>                   >>> midori
>                   >>> _______________________________________________
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>