[Annotation] annotating ribosomal proteins
Valerie Wood
val at sanger.ac.uk
Wed Jun 18 02:15:05 PDT 2008
I was thinking along the same lines, but that we could do IPI with
GO:complexID
I don't think we should use IDA. Up to now, where there is no direct
evidence for the process, I have used IC from GO:complexID for the
process if the inference can be made from an IDA to a complex, but this
is probably not ideal.
Val
Midori Harris wrote:
> 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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Valerie Wood Tel: 01223 496909
S. pombe Genome Project Fax: 01223 494919
Wellcome Trust Sanger Institute email: val at sanger.ac.uk
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