[Annotation] [Refgenome] Process annotation for ribosomal proteins
Judith Blake
jblake at informatics.jax.org
Sun Aug 31 08:58:43 PDT 2008
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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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