[Annotation] annotating ribosomal proteins

[Doug howe]

You could IPI the process only if they actually did experiments showing 
a role for the gene in the process..it doesn't sound like they have 
shown that in the paper.

Pascale Gaudet wrote:
> Can you then IPI the process?
>
> Doug howe wrote:
>> 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