[Annotation] Process annotation for ribosomal proteins
Rama Balakrishnan
rama at genome.stanford.edu
Fri Aug 29 14:11:27 PDT 2008
Considering that ribosomal genes are the Ref.Genome targets for Aug, I
would like to revive this discussion.
There was no clear answer on what evidence code is best for PROCESS
annotation in a situation where all you know is that the protein is a
subunit of a larger well established complex?
Here is Karen's summary of the whole issue.
>
> We don't have a problem with the complex annotation. It's fine to
> say that protein/gene X is in a complex by IDA.
>
> Our issue is with the process annotations for things where the only
> thing you know is that it is part of a complex, e.g. RPS25A is part
> of the ribosome, or UTP21 is part of the 90S preribosome. For both
> of these proteins, the sum total of the available experimental
> evidence is that they are part of the specified complex. There is no
> individual biochemical or genetic characterization. Nevertheless,
> the researchers who work on these complexes feel that being part of
> a big complex, whose function is known, e.g. translation for the
> ribosome and ribosome biogenesis and assembly for the 90S
> preribosome, is good evidence that a given gene product participates
> in that process.
>
> Before the 2006 Annotation Camp decision that IPI could only be used
> when you know it is direct, we used to use IPI for the process
> annotations. Now, I'm not really sure what evidence code to use in
> order to be able to annotate UTP21 to the process of "ribosome
> biogenesis and assembly". Since I can't put anything specific in the
> with field because I only know that UTP21 is part of the complex,
> but not whether it interacted specifically with any of the tagged
> proteins used to pull it down, we don't use IPI anymore. The
> experiment showed that UTP21 came down in the 90S preribosome
> complex, but while this is IDA for the component annotation, is it
> IDA for the process annotation?
>
> It has also been suggested to use IC from the GOID from the
> component term. However, this hides the fact that there is an
> experimental basis to believe that protein X is involved in a
> process Y. We're really not keen on this idea.
>
> To me, it seems that IPI is really the best explanation of the type
> of evidence for the process annotation, i.e. we know that protein X
> physically interacts with these other gene products as part of
> complex Z. I think we should either go back to the pre-2006 Annot
> Camp guidelines for IPI, which did NOT require direct interaction,
> or allow some form of complex ID in the with field to cover these
> situations.
>
> -Karen
I would greatly appreciate your feedback.
Thanks,
Rama
>
>> Judy
>>> To use the 'co-localizes' qualifier to qualify the identifier in
>>> the with/from column, which is basically supporting information
>>> for the evidence code, would be a very different use of the
>>> qualifier. We have previously decided that we did not want to mix
>>> and match what these qualifiers meant because it would be confusing.
>>> Considering that the ID put in the with column is supporting
>>> evidence, I think that it would be OK to allow IPI with "GOID for
>>> a complex" to include both where the annotated gene product is
>>> part of the complex and where the annotated gene product interacts
>>> with the complex. In the specific example brought up, we are
>>> talking about making a process annotation, and I think that it
>>> would be valid to make process annotations based either on a given
>>> gene product being in a complex or interacting with it.
>>> -Karen
>>> On Fri, 27 Jun 2008, Judith Blake wrote:
>>>> 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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