[Annotation] annotating ribosomal proteins
Karen Christie
kchris at genome.stanford.edu
Wed Jun 18 10:16:36 PDT 2008
we're talking about the process annotations (and the contributes to
qualifier is valid only for function) and which evidence code to use.
-K
On Wed, 18 Jun 2008, hjd at informatics.jax.org wrote:
> 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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