[Annotation] check for ND + additional annotation

[Valerie Wood]

In addition, related issue, can we have some guidelines for making  
mapping to the root node
using IEA (I don't think this should be done). See recent item on the 
annotation tracker

https://sourceforge.net/tracker/?func=detail&atid=605890&aid=1978965&group_id=36855


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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>>> >
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>>> >
>>>   
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>>>
>>>
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>>
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>
>


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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
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Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe



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