[Annotation] annotating ribosomal proteins
Judith Blake
jblake at informatics.jax.org
Fri Jun 27 12:09:15 PDT 2008
Karen,
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".
yes that's what I mean. ESF2 colocalizes with the 90S preribosome where
the ESF2 is annotated to the GO term 90S preribosome.
Now.
the evidence for that might be an IPI, yes?
IPI with what?
with the 902 preribosome. This 90S preribosome is a 'complex'. I
think in following through on this, the complexes would need to be
distinguishable from other CC terms.
The above would distinguish gp involved in complexes from a gp
associated with another gp by IPI and a gpID in the with field.
That's all from me on this. Maybe I'm missing something fundamental.
I was trying to think about distinctions. I'll talk with Harold :)
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
>>
More information about the Annotation
mailing list