[Annotation] [Refgenome] Process annotation for ribosomal proteins
Chris Mungall
cjm at berkeleybop.org
Sat Aug 30 11:23:31 PDT 2008
There should be a link in the ontology, ribosome functions_in protein
biosynthesis. Then the IC becomes redundant.
On Aug 29, 2008, at 10:31 PM, Harold Drabkin wrote:
> Rama Balakrishnan wrote:
>> 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?
>
> If for example, there is a good experimental to a complex like a
> ribosome, one could use an IC to translation based on the GO id for
> the ribosome and it's reference., I would think. Unfortunately for
> mouse, the ribosomal protein genes don't even have a real experiment
> to show they are in the ribosome 8-( Most cloned via sequence
> similarity etc. etc.
>
> hjd
>
>>
>> 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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