[Annotation] [Refgenome] Process annotation for ribosomal proteins
Chris Mungall
cjm at berkeleybop.org
Tue Sep 2 10:13:24 PDT 2008
On Sep 1, 2008, at 7:24 PM, Harold Drabkin wrote:
> 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.
OK
> At the moment, since we don't have these additional relationships, I
> think the IC is not redundant, and is safe.
Absolutely! I'm not suggesting holding off on adding these in the
short term. In fact the ICs will be useful for mining other possible
inter-ontology links.
>
> 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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>>>>>>
>>>>>> _______________________________________________
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>>>>>
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