[Annotation] annotating ribosomal proteins
Rama Balakrishnan
rama at genome.stanford.edu
Wed Jun 18 14:53:14 PDT 2008
Hi,
1) Although there is a REACTOME ID for the yeast ribosome complex, I
think a better solution would be to allow the GOID for the complex in
the 'with' column for IPI. This is because, Reactome has IDs only for
human and yeast, and this solution won't scale for other organisms.
2) If we move towards the idea of using IPI in this fashion, we also
need to update the documentation for IPI because by saying that the
subunit interacts physically with the complex, one could infer that
the subunit peripherally interacts with the complex as oppose to
inferring that the subunit is part of the complex.
Thanks,
Rama
On Jun 18, 2008, at 9:25 AM, D'Eustachio, Peter wrote:
>
> Hi, Midori,
>
> We do have such identifiers (though in general - this case is an
> exception - only for human proteins and complexes) and this sounds
> like a legitimate use of them, but it also seems like a kind of hack
> around the basic problem. Earlier in this thread, someone pointed to
> one paper that supports the assertion "ribosomes are required for
> translation to occur", and another that supports the assertion
> "subunit X is required for the assembly of a complete ribosome", but
> no single paper that asserts "the ribosomes that actually
> participate in translation have been shown to contain subunit X",
> and so we are left to draw this conclusion by inference, reading the
> two papers in succession. I guess all of this violates the principle
> that there should be a 1:1:1 mapping of protein : GO term :
> publication and evidence code. Here, Reactome has silently done the
> inference so formally you can make a 1:1:1 relationship, but there's
> still a hidden multi-step inference in there.
>
> That said, we live by that hack - our unit of curation is the
> reaction, and I have yet to find the reaction all of whose
> attributes can be annotated without combining evidence assertions
> inferentially from multiple papers.
>
> Peter
>
>
> -----Original Message-----
> From: annotation-bounces at genome.stanford.edu on behalf of Midori
> Harris
> Sent: Wed 6/18/2008 5:02 AM
> To: Karen Christie
> Cc: GO Annotation list
> Subject: Re: [Annotation] annotating ribosomal proteins
>
> 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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