[Annotation] [Refgenome] Process annotation for ribosomal proteins
Harold Drabkin
hjd at informatics.jax.org
Mon Sep 1 11:24:08 PDT 2008
The contributes_to was intended to be used to indicate that two or more
things were required to obtain an particular activity. It was not meant
to say that things contributed to a process.
Form the guide
"contributes_to may be used only with molecular function terms. "
If we confine our use of "contributes_to" to this rule, there will be
much less confusion about it's use as there seemed to be in the past.
At the moment, since we don't have these additional relationships, I
think the IC is not redundant, and is safe.
hjd
Chris Mungall wrote:
>
> 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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