[go] AmiGO and annotation qualifiers

[Pankaj Jaiswal]

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