[Annotation] annotating ribosomal proteins

[Karen Christie]

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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