[Annotation] annotating ribosomal proteins
Judith Blake
jblake at informatics.jax.org
Fri Jun 27 09:18:57 PDT 2008
Here's what I was thinking.
IPI for the binding
with the GO:complexID in the "with" field
and the 'co-localizes' as the qualifier.
Thus, the gene product 'colocalizes' with 'complexID' by evidence code 'IPI'
which is different than
Rama Balakrishnan wrote:
> 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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