[Annotation] annotating ribosomal proteins
hjd at informatics.jax.org
hjd at informatics.jax.org
Wed Jun 18 10:02:47 PDT 2008
I would think the individual members of the complex would an a
contribute_to qualifer for the activity term annotation, with each member
having a component annotation to the complex. That way no one would be
confused into thinking that the particuarl protein had the activity all by
itself.
hjd
> Hi,
>
> I don't think I can contribute anything but more questions to this
> discussion, but would really like to know the answers. First of all, I
> could absolutely swear that not too long ago, I saw a sentence somewhere
> in the annotation documentation saying something along the lines of, if
> a complex has a function, the function is transferred to its subunits.
> (Maybe it was about process, I don't recall.) However, I can not find
> this anywhere any more. It is very important to us to know the answer
> to this; in EcoCyc, I have the ability to annotate complexes themselves
> with GO terms, and I think those become attached to the individual gene
> products for the mapping file.
>
> While poking around in the guide, I only found a couple of relevant
> references to protein complexes. Under "Valid Function Terms" in
> http://geneontology.org/GO.function.guidelines.shtml, it says this:
> "Functions are not restricted to the activities of single gene products;
> multi-gene product complexes can also have functions." That's generous
> :-) , but no word on how to transfer those functions to single gene
> products. There is also a section on "Function Terms for Subunits",
> which refers to the GO annotation guide for advice on how to annotate
> subunits of a complex - in this case, referring to itself is not
> entirely useful.
>
> From the discussion so far, my take-home message was that one should
> never annotate components of a complex to a process or function of the
> complex with IDA. Is this the correct impression? If yes, then looking
> at this the other way, any function/process that is performed by a
> multi-subunit complex will never have an IDA annotation. No more IDAs
> for translation, replication, transcription,...?
>
> Aside from my IDA concerns, would it be possible to use IMP? Granted,
> if the mutant phenotype is death, that's not very interesting (Botstein
> said so himself) nor very informative in and of itself, but if a protein
> is part of the ribosome and you can't knock out the gene without killing
> the cell, would it be a safe assumption that said subunit is involved in
> translation? (I think there *are* non-essential ribosomal subunits,
> which would then not get the translation term.)
>
> -Ingrid
>
> Valerie Wood wrote:
>>
>> I was thinking along the same lines, but that we could do IPI with
>> GO:complexID
>>
>> I don't think we should use IDA. Up to now, where there is no direct
>> evidence for the process, I have used IC from GO:complexID for the
>> process if the inference can be made from an IDA to a complex, but
>> this is probably not ideal.
>>
>> Val
>>
>> Midori Harris wrote:
>>> 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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>>
>>
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