[Annotation] [Evidence] annotating ribosomal proteins

[Valerie Wood]

>
> It has also been suggested to use IC from the GOID from the component 
> term. However, this hides the fact that there is an experimental basis 
> to believe that protein X is involved in a process Y. We're really not 
> keen on this idea.
>
> To me, it seems that IPI is really the best explanation of the type of 
> evidence for the process annotation, i.e. we know that protein X 
> physically interacts with these other gene products as part of complex 
> Z. I think we should either go back to the pre-2006 Annot Camp 
> guidelines for IPI, which did NOT require direct interaction, or allow 
> some form of complex ID in the with field to cover these situations.
>
> -Karen
>
>

I would still  be comfortable with IC.

I don't think that it hides the fact that there is an experimental basis 
for the annotation.
if a gene product has function A
and a curator can infer that
gene which has function A has process B, then this must be true every 
time function A occurs (otherwise the curator could not make the inference).
The experimental basis has to exist, and so is implicit in the use of 
the evidence code.

However, the name of the evidence code implies the curator made the 
deduction rather than the author.
Clearly when an author identifies a gene product as part of the ribosome 
they are implicating it in translation,
and are implicating UTP21 in ribosome biogenesis and assembly. When we  
make an IC annotation, we are *always* making an inference that the 
author would make themselves  (I hope), based on the existing biology 
but have not shown directly. Perhaps the scope of "IC" could be 
broadened (or changed to what it really means, which is
"inferred from an experimental GO annotation"

These annotations could be used to seed the inter-ontology links, 
because we are saying
complex A is always involved in process B
or
function C is always involved in process D
If this turns out to be incorrect then either
a) the annotation should not have been made in the first place, OR
b) new biology has shown that, in fact, not all ribosomal subunits are 
involved in translation

I have used both methods to make these types of process annotations (IPI 
with a gene product, and IC with a GO term), but it would be good to 
have a recommended and consistent method. The worst solution would be to 
use IDA if there is no direct evidence for a role in the process being 
annotated, as this implies a greater degree of knowledge than complex 
membership.


val








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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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