[Annotation] [Refgenome] Process annotation for ribosomal proteins
Chris Mungall
cjm at berkeleybop.org
Mon Sep 1 10:57:04 PDT 2008
On Aug 31, 2008, at 4:58 PM, 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]
On second thoughts, erhaps the safest inference here is one of
contributes_to?
David, Tanya and I came up with some proposed rules for combining
relations. For example, chaining located_in with functions_in would
yield contributes_to
See:
http://wiki.geneontology.org/index.php/Relation_composition
Particularly:
http://wiki.geneontology.org/index.php/Relation_composition#rules_involving_gene_products
We can make stronger relations if need be. For example, a relation for
stating that every part of the ribosome functions_in biosynthesis (if
this happens to be true). Then we can make a stronger inference about
gene products located in the 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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