[Annotation] check for ND + additional annotation

[Midori Harris]

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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