[Annotation] annotating ribosomal proteins

[Karen Christie]

Hi Pascale,

Rama is looking at the original papers, and ribosomes and the processes of 
ribosome assembly are probably better characterized in cerevisiae than in 
any other eukaryote.

The real issue here is that what has been shown is that protein X is part 
of a big complex, e.g. the ribosome, for which the function is known. The 
sum total of the experimental evidence available for a significant number 
of ribosomal proteins is that they are purified as part of the ribosome 
complex. So, for component, it's easy. This is IDA evidence that protein X 
is in the ribosome, or in the Small SubUnit (SSU) or in the Large SubUnit 
(LSU), or whatever complex is characterized.

But is being in the ribosome considered to be IDA evidence for a process 
annotation to translation? In one way of looking at it, the direct assay 
is that it's part of a complex and then you're assuming that the 
individual protein is involved in translation because it's in that 
complex. Is this a direct assay for being involved in translation? Can we 
use IDA for a process annotation? or is it a more accurate statement to 
say that the IDA is just for the annotation to the complex term and then 
use IC from the complex term for the Process annotation?

-Karen



On Tue, 17 Jun 2008, Pascale Gaudet wrote:

> Hi Rama,
> 
> I think this is a perfect case where one of us should go back to the original papers and find
> what we all need to ISS to (in which organism the funtion and process were shown).
> 
> Pascale
> 
> Rama Balakrishnan wrote:
>       Hi,
>
>       I have couple of ribosomal proteins to annotate as part of the ref-genome curation
>       project. Turns out that there is no direct experimental evidence showing that these
>       proteins are involved in translation. Almost all the studies purify the ribosome
>       from yeast and identify the subunits by one or more techniques.
>
>       I can do IDA for CC annotation, that is straightforward. Is IDA for function
>       annotation- structural constituent of ribsomome okay? What about BP? I can do IC
>       from the CC term, but that is not direct experimental evidence. What do you all
>       think?
>
>       Thanks for your time,
>
>       Rama
>
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>