[Annotation] annotating ribosomal proteins

[Midori Harris]

Reactome has identifiers for complexes ... could you use IPI with the 
Reactome ID for the ribosome? (E.g. S. cerevisiae ribosome is 
Reactome:141693; H. sapiens is 72500.)

If this is a stupid idea, I'll bow out quietly ... it's been a long, long 
time since I did annotation.

m

On Tue, 17 Jun 2008, Karen Christie wrote:

> As of the 2006 Annotation camp, we agreed that IPI could only be used when 
> you know it is a direct interaction and that you should fill the with column 
> with the directly interacting gene products.
>
> Prior to that, I often used to use IPI for the proteins that came down in a 
> complex, and for 'modern' purifications where one protein was tagged, I'd put 
> that one in the with column. But we agreed that it isn't known that this is 
> direct, so we quit doing it. I've been having the same problem with 
> spliceosomal complexes and have become rather unkeen on the decision that IPI 
> could only be used for known direct interactions. It seems that this 
> requirement got added by the people who want to use the IPI with field as a 
> protein-protein interaction database.
>
> Anyway, I thought that IPI with the tagged protein seemed like a much better 
> representation of the evidence for the process than IDA. Coming down as part 
> of a complex doesn't seem like a direct assay for process. IPI with one of 
> the proteins in the complex seems like a better representation of what was 
> actually done, but we can't do now that because of the direct interaction 
> requirement.
>
> IC also seems a little unsatisfying, since it's not experimental. I don't 
> know, maybe for complexes as well characterized as the ribosome, or the 
> spliceosome, just being in the complex is direct evidence that it's part of 
> the process that the complex is experimentally characterized to be part of...
>
> I've been a bit muddled about how best to deal with these ever since the 2006 
> Annotation camp. I liked using IPI better than IDA...
>
> -Karen
>
>
> On Tue, 17 Jun 2008, 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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>> 
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