[Annotation] annotating ribosomal proteins

[Rama Balakrishnan]

There is a 1978 paper (PMID: 355832) where the authors have purified  
the yeast ribosome and showed that the entire complex translates. But  
that paper doesn't tell me if the subunits I am interested in are in  
the complex.

Rama


On Jun 17, 2008, at 4:09 PM, Karen Christie wrote:

> 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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