[Annotation] annotating ribosomal proteins
Judith Blake
jblake at informatics.jax.org
Wed Jun 25 04:51:40 PDT 2008
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?
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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