[Annotation] annotating ribosomal proteins
Valerie Wood
val at sanger.ac.uk
Thu Jul 3 02:11:13 PDT 2008
HI Karen,
yes this is true.
I was trying to say that those of us who use IPI to capture direct
interactions, it will still be possible to distinguish these.
Val
Karen Christie wrote:
> As I understand it, use of IPI evidence is not currently restricted to
> function (binding) annotations. At the 2006 Annotation Camp, we
> discussed that it might be appropriate to use IPI evidence for a
> process term, depending on how well characterized the protein referred
> to in the with column is.
>
> -Karen
>
> On Mon, 30 Jun 2008, Valerie Wood wrote:
>
>>
>> I think what Karen proposes would be a good solution. It would be
>> confusing to allow 'co-localizes' to have a totally different
>> meaning, and this should continue to be remain restricted to
>> component annotations.
>>
>> This proposal would allow us to distinguish direct physical
>> interactions, captured using the protein binding (or one of its
>> children) function term, from 'guilt by association' process
>> annotations, where a gene product is implicated in a biological
>> process because it is a member of a specific complex.
>>
>> the 'with' field would continue to be mandatory for IPI, and it
>> would be:
>>
>> i) a gene product when supporting a function (binding ) annotation,
>> ii) a GO:component or gene product when supporting a process annotation
>>
>> Val
>>
>>
>>
>>
>> Karen Christie wrote:
>>> Hi Judy,
>>>
>>> I really don't think we should use the 'co-localizes' qualifier in
>>> this way. Currently, when the 'co-localizes' qualifier is used (only
>>> allowed for component annotations), it means that the annotated gene
>>> product co-localized with the object indicated by the GO term to
>>> which it was annotated, e.g. ESF2 colocalizes with the 90S
>>> preribosome, where the ESF2 gene is annotated to the GO term "90S
>>> preribosome".
>>>
>>> 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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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
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>>>>>>>>>>>
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>>
>>
>> --
>> ---------------------------------------------------------------------------
>>
>> Valerie Wood Tel: 01223 496909
>> S. pombe Genome Project Fax: 01223 494919 Wellcome Trust
>> Sanger Institute email: val at sanger.ac.uk
>> Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe
>> Hinxton, Cambridge, CB10 1HH
>> http://www.sanger.ac.uk/Projects/S_pombe
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>
>
>
--
---------------------------------------------------------------------------
Valerie Wood Tel: 01223 496909
S. pombe Genome Project Fax: 01223 494919
Wellcome Trust Sanger Institute email: val at sanger.ac.uk
Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe
Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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