[Annotation] annotating ribosomal proteins
Rama Balakrishnan
rama at genome.stanford.edu
Tue Jun 24 13:57:28 PDT 2008
Hi all,
I am sure all the other groups annotating ribosomal genes are facing
the same issue. I would like to hear from you about the new proposal
for IPI or if you have other suggestions.
Thanks,
Rama
On Jun 18, 2008, at 2:53 PM, Rama Balakrishnan wrote:
> 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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