[Annotation] annotating ribosomal proteins
Karen Christie
kchris at genome.stanford.edu
Fri Jun 27 09:52:19 PDT 2008
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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