[Annotation] annotating ribosomal proteins
Ingrid Keseler
keseler at AI.SRI.COM
Wed Jun 18 08:58:40 PDT 2008
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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