[Annotation] annotating ribosomal proteins
Rama Balakrishnan
rama at genome.stanford.edu
Thu Jun 26 12:20:50 PDT 2008
Hi Judy,
Comment below.
On Jun 25, 2008, at 4:51 AM, Judith Blake wrote:
> Rama,
>
> I agree that the solution needs to go beyond ReactomeIDs. However,
> there are many other complex resources, and my summer intern is in
> the process of collecting a more global (one would hope
> comprehensive) list of complexes with IDs from these other
> resources. So putting a complex ID in the 'with' field seems
> correct. And allowing the GO:ID seems correct too
>
> I think distinguishing between 'member of complex' and 'interacts
> with complex' is very important. The CC assignment places a gp in
> a complex. I think using the IPI code here, while technically
> defensible, might result in the confusion. Would this be a place
> that IPI with 'co-localizes' would clarify the distinction?
Hmm...I don't think I follow your last sentence completely.
So far, we have used Qualifiers to qualify the GO term and not the
evidence. And we don't use qualifiers for Process terms.
Contributes_to is specifically meant for Function, and co_localizes is
meant for CC.
Thanks,
Rama
>
>
> judy
>
> Rama Balakrishnan wrote:
>> 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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>>>>>>
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>>>>>>
>>>>>>
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