[Annotation] annotating ribosomal proteins

[Doug howe]

I think:
"the IDA is just for the annotation to the complex term and then use IC 
from the complex term for the Process annotation"
is the way to go.

Doug

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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>>
>>
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-- 
Doug Howe, Ph.D.
ZFIN Scientific Curator
Zebrafish Nomenclature Coordinator