[go] AmiGO and annotation qualifiers

[Judith Blake]

I think by far the most common case right now is not with isoforms, but 
with conflicting data.  And that should be represented.

Judy

Pankaj Jaiswal wrote:
>
>
> Judith Blake wrote:
>> hummm
>> I think the case that Harold was saying, and that we currently have 
>> in other annotations here at MGI, is that we have
>>
>> x A
>> x NOT A
>>
>> both lines of evidence exist at this point.
>>
>> In some cases, different experiments give different results
>>
>> In the case that Harold discussed, the issue really was that we don't 
>> properly distinguish isoforms, so from the gene level, the two are 
>> combined whereas if you could represent each isoform, the one would 
>> be x-1 A and one would be x-2 NOT A.
>>
>> judy
>>
>
> I think unless the correct object_type is not defined in the 
> annotations, it may not be very obvious. Ideally annotations should 
> not be done to the gene, but to the transcripts/proteins or their 
> isoforms (means all coming from the same gene/loci on the genome).
>
> So it can be
>
> x.1 (object_type: protein isoform) and x.2 (object_type: protein 
> isoform) map to x (object_type: gene)
>
> Annotations
>
> x.1 A
> x.2 NOT A
>
> Or
>
> x A With x.1
> x NOT A With x.2
>