[Annotation] [Refgenome] Process annotation for ribosomal proteins
Harold Drabkin
hjd at informatics.jax.org
Mon Sep 1 10:30:55 PDT 2008
No, I am only doing F x P for various metabolic pathways.
Linking "ribosome' to "translation via "functions_in" and doing similar
things would be a nice idea.
hjd
Judith Blake wrote:
> so this then would be
>
> ribosome gene product 'located_in' GO:complex 'ribsome', ribosome
> 'functions_in" protein biosynthesis
>
> [implication that therefore ribosome gene product functions in
> BP:protein biosynthesis by reason of its location in the CC:ribosome]
>
> and yes, then IC redundant.
>
> So Harold is making a draft file of relationships for F::P, but,
> Harold, are you also doing C:P ?
>
> until these new relationships are implemented, I agree with Harold
> that IC would be appropriate evidence code.
>
> Judy
>
>
> Chris Mungall wrote:
>>
>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>>>>> ------------------------------------------------------------
>>>>>>>>>>>>> This email message, including any attachments, is for the
>>>>>>>>>>>>> sole use of the intended recipient(s) and may contain
>>>>>>>>>>>>> information that is proprietary, confidential, and exempt
>>>>>>>>>>>>> from disclosure under applicable law. Any unauthorized
>>>>>>>>>>>>> review, use, disclosure, or distribution is prohibited. If
>>>>>>>>>>>>> you have received this email in error please notify the
>>>>>>>>>>>>> sender by return email and delete the original message.
>>>>>>>>>>>>> Please note, the recipient should check this email and any
>>>>>>>>>>>>> attachments for the presence of viruses. The organization
>>>>>>>>>>>>> accepts no liability for any damage caused by any virus
>>>>>>>>>>>>> transmitted by this email.
>>>>>>>>>>>>> =================================
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Annotation mailing list
>>>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>> _______________________________________________
>>>>>>>> Annotation mailing list
>>>>>>>> Annotation at geneontology.org
>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>
>>>>>>
>>>>
>>>> _______________________________________________
>>>> Refgenome mailing list
>>>> Refgenome at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/refgenome
>>>
>>> _______________________________________________
>>> Refgenome mailing list
>>> Refgenome at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/refgenome
>>>
>>
>> _______________________________________________
>> Refgenome mailing list
>> Refgenome at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/refgenome
More information about the Annotation
mailing list