[Annotation] check for ND + additional annotation

[Stacia Engel]

yes, there are several IEAs from UniProtKB and one RCA from  
bioPIXIE.  the gene is CWC23:

http://db.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?dbid=CWC23


On Sep 4, 2008, at 4:51 AM, Midori Harris wrote:

> 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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