[Annotation] check for ND + additional annotation

[Judith Blake]

hummm

yah it makes sense in that there is no experimental data.  no it does 
not make sense when there is a computational annotation.

one way around this is that the ND genes should be (and are in MGI) 
tagged as 'complete'.  That means that the literature has been 
reviewed.  Then the database has a mechanism for adding new literature 
tags (pubmedIDs) to a file when a new publication is identified for that 
gene.  In this way, the ND designation disappears in the annotation 
file, the gene is marked as 'complete', and the  ongoing QC report 
alerts curators as to when experimental literature enters the system.

here's a example from our 'complete' QC file.  'outstanding refs' are 
jnum (our lit number, tied to PubmedID) added to MasterBib after the 
'Data_complete'.  These are cases where the new literature needs to be 
curator to maintain the 'complete' status.

The columns are

Gene Symbol   
MGI-ID   
reference gene status   
Date_complete   
#Refs_used   
outstanding_refs

in this list, the 'y' mean that it is a designated ref gene.  Genes on 
this list with 'n' are, for example, genes with ND that have not been 
chosen as a reference genome gene, but are on the 'complete' list for 
us.  You can also see here for Aggf1, a ref genome gene, that we have no 
literature.

Judy

cvr1b    MGI:1338944    y    04/19/2007    6   
Acvr2a    MGI:102806    y    03/06/2008    12   
Acvr2b    MGI:87912    y    04/16/2008    16   
Acvrl1    MGI:1338946    y    04/09/2008    5   
Ada    MGI:87916    y        13    13
Adh1    MGI:87921    y        5    18
Adh4    MGI:1349472    y    03/03/2008    2   
Adh5    MGI:87929    y    02/29/2008    5   
Adh7    MGI:87926    y    03/12/2008    9   
Adhfe1    MGI:1923437    y    02/05/2008    2   
Adsl    MGI:103202    y    06/14/2007    1   
Adss    MGI:87948    y    05/02/2008    2   
Adssl1    MGI:87947    y    05/08/2008    3   
Aggf1    MGI:1913799    y    06/14/2007    0   
Agl    MGI:1924809    y    04/09/2008    3   
Agxt    MGI:1329033    y    10/15/2007    2   
Alas2    MGI:87990    y    10/15/2007    4    J:127025,J:130852
Alb    MGI:87991    y    08/11/2007    6    
J:123909,J:129068,J:132868,J:134487
Aldh5a1    MGI:2441982    y    03/28/2008    10   
Alg12    MGI:2385025    y    04/06/2007    1   





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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