[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Judith Blake
jblake at informatics.jax.org
Fri Jun 6 10:53:24 PDT 2008
that's where i started...not explicit enough for the other evidence
codes, yet an experiment done in that organism (one thinks mostly)
EXP
judy
Pascale Gaudet wrote:
> me too.
>
> Susan Tweedie wrote:
>> I like EXP best too.
>>
>> Susan
>>
>> On Fri, 2008-06-06 at 12:45 -0400, Gwinn Giglio, Michelle wrote:
>>
>>> Hi all,
>>>
>>> I also think EXP is appropriate here. I worried about using either TAS or
>>> NAS (in addition to not being consistent with the documentation) because
>>> those codes do not indicate that an experiment was done and I think its
>>> important to capture that. So I like the idea of EXP and although I know
>>> that many are worried about a slippery slope here, I think that this shows a
>>> way in which the EXP code is very useful. If an experiment does not fit
>>> well into one of the 5 experimental codes then I see nothing wrong with
>>> using EXP. The alternative is to make yet more codes (ISE, inferred from
>>> Southern experiment) which I think we want to avoid.
>>>
>>> Michelle
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 6/6/08 12:39 PM, "Karen Christie" <kchris at genome.stanford.edu> wrote:
>>>
>>>
>>>> Based on our current documentation of either TAS or NAS, this is just not
>>>> an author statement because either TAS or NAS is intended for things NOT
>>>> shown in the paper being cited. Use of either is a misrepresentation of
>>>> the fact that there is experimental evidence.
>>>>
>>>> Yesterday in SGD's curator meeting, there was sentiment that use of EXP
>>>> should be avoided, but in thinking more, I have come to the opinion that
>>>> this is the only currently available code that is not a misrepresentation
>>>> of the evidence. I should make it clear that I am speaking for myself and
>>>> not for SGD in that statment, but the evidence in this paper is just not
>>>> an author statement of any kind as we've conceived of these evidence
>>>> codes. I think it would be really poor practice to start kludging
>>>> inappropriate stuff into the author statement codes right after we just
>>>> spent a year cleaning up the documentation and making it sensible.
>>>>
>>>> -Karen
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, 6 Jun 2008, Judith Blake wrote:
>>>>
>>>>
>>>>> I think TAS is really it. Southerns don't directly show by sequence
>>>>> similarity nor by IPI. TAS says the author says so. The fact that there
>>>>> isn't a way to capture Why he/she says so, isn't in our system.
>>>>>
>>>>> Judy
>>>>>
>>>>> Karen Christie wrote:
>>>>>
>>>>>> Our new documentation for the distinction between TAS and NAS is very
>>>>>> simple. If they cite another paper, it is TAS. If it isn't tracable to
>>>>>> another publication, then it isn't TAS.
>>>>>>
>>>>>> Here's what we have on the web in the current documentation:
>>>>>>
>>>>>> TAS
>>>>>> Any statement in an article where the original evidence (experimental
>>>>>> results, sequence comparison, etc.) is not directly shown, but is
>>>>>> referenced in the article and therefore can be traced to another source.
>>>>>>
>>>>>> NAS
>>>>>> Statements in papers (abstract, introduction, or discussion) that a curator
>>>>>> cannot trace to another publication
>>>>>>
>>>>>> -Karen
>>>>>>
>>>>>>
>>>>>> On Thu, 5 Jun 2008, Stacia Engel wrote:
>>>>>>
>>>>>>
>>>>>>> I agree that it should be TAS with the paper that does the Southern. NAS
>>>>>>> doesn't make much sense.
>>>>>>>
>>>>>>> stacia
>>>>>>>
>>>>>>>
>>>>>>> On Jun 5, 2008, at 3:37 PM, MICHELLE GIGLIO wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> Should we explore the option of expanding the scope of IPI? A Southern
>>>>>>>> is an experiment that looks for a physical interaction.
>>>>>>>>
>>>>>>>> But if folks don't want to do that, then I think it would be TAS, not
>>>>>>>> NAS. It is traceable to the Southern.
>>>>>>>>
>>>>>>>> Michelle
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: annotation-bounces at genome.stanford.edu on behalf of Karen Christie
>>>>>>>> Sent: Thu 6/5/2008 4:53 PM
>>>>>>>> To: Pascale Gaudet
>>>>>>>> Cc: GO Annotation list; Julie Park; evidence at genome.stanford.edu
>>>>>>>> Subject: Re: [Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
>>>>>>>>
>>>>>>>> How could we cite SGD? We didn't do any sequence similarity comparisons.
>>>>>>>>
>>>>>>>> Also, why do you think the Southern evidence is dubious? High stringency
>>>>>>>> Southerns are actually quite strong evidence.
>>>>>>>>
>>>>>>>> -Karen
>>>>>>>>
>>>>>>>> On Thu, 5 Jun 2008, Pascale Gaudet wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> Another suggestion: How about making the annotation citing SGD rather
>>>>>>>>> than the paper? Is the sequence similarity good enough to do that?
>>>>>>>>>
>>>>>>>>> It seems to me that Southern evidence is pretty dubious anyway, I know
>>>>>>>>> it's nice to capture all information we can get from papers, but that
>>>>>>>>> seems
>>>>>>>>> rather low quality?
>>>>>>>>>
>>>>>>>>> Pascale
>>>>>>>>>
>>>>>>>>> Julie Park wrote:
>>>>>>>>> Thanks all for your input.
>>>>>>>>>
>>>>>>>>> Unfortunately there is no other evidence for these annotations and all
>>>>>>>>> subsequent papers that discuss these genes reference the original
>>>>>>>>> Southern
>>>>>>>>> experiments.
>>>>>>>>>
>>>>>>>>> The curators here agree with Emily's reasoning for not using EXP. We
>>>>>>>>> also are against using IPI. Since both interacting parties are DNA
>>>>>>>>> molecules and not gene products it is both misleading and non-compliant
>>>>>>>>> with the IPI criteria.
>>>>>>>>>
>>>>>>>>> We at SGD have decided that given the changes to the ISS evidence code,
>>>>>>>>> we'll change these annotations to use the evidence code NAS and still
>>>>>>>>> use
>>>>>>>>> the Southern paper as the reference.
>>>>>>>>>
>>>>>>>>> Thanks again,
>>>>>>>>> -Julie
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> From: Emily Dimmer <edimmer at ebi.ac.uk>
>>>>>>>>> Date: June 5, 2008 4:56:56 AM PDT
>>>>>>>>> To: Evidence Code Group <evidence at genome.stanford.edu>
>>>>>>>>> Cc: GO Annotation list <annotation at genome.stanford.edu>
>>>>>>>>> Subject: Re: [Evidence] [Annotation] Fwd: ISS/ISA from Southerns?
>>>>>>>>>
>>>>>>>>> I like the idea of using IPI.
>>>>>>>>>
>>>>>>>>> At the moment all experimental annotations should be able to be
>>>>>>>>> described by one of the child codes of EXP, the only annotations
>>>>>>>>> which directly use this code are those which do meet the criteria of the
>>>>>>>>> child experimental codes, but cannot be retrofitted by the
>>>>>>>>> submitting group.
>>>>>>>>> It might be nice to keep it this way, rather than allow EXP to be used
>>>>>>>>> for undocumented experimental methods - otherwise EXP could
>>>>>>>>> potentially end up as a dumping ground for a diverse range of
>>>>>>>>> annotations where the curator is not sure which of the child
>>>>>>>>> experimental codes is appropriate.
>>>>>>>>>
>>>>>>>>> Emily
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Judith Blake wrote:
>>>>>>>>> I agree too. This is too far from ISS as now employed.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> aren't these from older papers? Isn't there better evidence
>>>>>>>>> available now? if so, why include them? if not, what about
>>>>>>>>> EXP?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> judy
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> MICHELLE GIGLIO wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Rama,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I agree with Susan. I am reluctant to add this back to ISS.
>>>>>>>>> However, I don't know where it would go
>>>>>>>>> instead.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> If it does come back to the ISS family (if we can not think
>>>>>>>>> of another alternative) then it definitely can
>>>>>>>>> NOT go under ISA as there is no alignment in this situation.
>>>>>>>>> It would have to be plain ISS. (But I still
>>>>>>>>> don't like it there.)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Could it possibly be an IPI?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Michelle
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -----Original Message-----
>>>>>>>>>
>>>>>>>>> From: evidence-bounces at genome.stanford.edu on behalf of
>>>>>>>>> Susan Tweedie
>>>>>>>>>
>>>>>>>>> Sent: Wed 6/4/2008 5:17 AM
>>>>>>>>>
>>>>>>>>> To: Rama Balakrishnan
>>>>>>>>>
>>>>>>>>> Cc: Evidence Code Group; GO Annotation list
>>>>>>>>>
>>>>>>>>> Subject: Re: [Evidence] Fwd: ISS/ISA from Southerns?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> One thing we'd have to consider if we added this (back?) to
>>>>>>>>> ISS is that
>>>>>>>>>
>>>>>>>>> the new classification of evidence codes groups ISS, ISA etc
>>>>>>>>> as
>>>>>>>>>
>>>>>>>>> 'computational analysis evidence codes' - that wouldn't be
>>>>>>>>> strictly true
>>>>>>>>>
>>>>>>>>> if Southerns were included.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I am uneasy about mixing together cases where the sequence
>>>>>>>>> is known with
>>>>>>>>>
>>>>>>>>> those that aren't - no review of the evidence is possible in
>>>>>>>>> the latter
>>>>>>>>>
>>>>>>>>> case. Personally, I would be reluctant to make an annotation
>>>>>>>>> based on a
>>>>>>>>>
>>>>>>>>> cross-hybridisation expt but maybe I just remember too many
>>>>>>>>> spurious
>>>>>>>>>
>>>>>>>>> bands from my time in the lab.
>>>>>>>>>
>>>>>>>>> Are there really that many cases these days where sequencing
>>>>>>>>> is so
>>>>>>>>>
>>>>>>>>> stnadard where this is the only evidence to support a term?
>>>>>>>>> Maybe I'm
>>>>>>>>>
>>>>>>>>> just spolit working on a species with complete genome
>>>>>>>>> sequence...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Susan
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> I haven't heard from anybody on this so far. Is it okay if
>>>>>>>>>>
>>>>>>>>> we add
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> 'southern analysis' as an acceptable evidence to the ISS
>>>>>>>>>>
>>>>>>>>>> documentation?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Rama
>>>>>>>>>>
>>>>>>>>>> Begin forwarded message:
>>>>>>>>>>
>>>>>>>>>>> From: Rama Balakrishnan <rama at genome.stanford.edu>
>>>>>>>>>>>
>>>>>>>>>>> Date: May 9, 2008 5:18:06 PM PDT
>>>>>>>>>>>
>>>>>>>>>>> To: Evidence Code Group <evidence at genome.stanford.edu>
>>>>>>>>>>>
>>>>>>>>>>> Cc: GO Annotation list <annotation at genome.stanford.edu>
>>>>>>>>>>>
>>>>>>>>>>> Subject: [Evidence] ISS/ISA from Southerns?
>>>>>>>>>>>
>>>>>>>>>>> Reposting...
>>>>>>>>>>>
>>>>>>>>>>> I am dealing with a similar situation like the one Julie
>>>>>>>>>>>
>>>>>>>>> has
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> mentioned below.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Rama
>>>>>>>>>>>
>>>>>>>>>>> Begin forwarded message:
>>>>>>>>>>>
>>>>>>>>>>>> From: Julie Park <juliep at genome.stanford.edu>
>>>>>>>>>>>>
>>>>>>>>>>>> Date: April 23, 2008 3:57:22 PM PDT
>>>>>>>>>>>>
>>>>>>>>>>>> To: evidence at genome.stanford.edu
>>>>>>>>>>>>
>>>>>>>>>>>> Subject: [Evidence] ISS/ISA from Southerns?
>>>>>>>>>>>>
>>>>>>>>>>>> Dear evidence code group,
>>>>>>>>>>>>
>>>>>>>>>>>> I had a question about whether Southern analysis alone
>>>>>>>>>>>>
>>>>>>>>> can be used
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> as > > > evidence for an annotation.
>>>>>>>>>>>>
>>>>>>>>>>>> In S. cerevisiae, MEL2-10 are annotated by ISS to
>>>>>>>>>>>>
>>>>>>>>>>>> alpha-galactosidase > > > activity. There is no
>>>>>>>>>>>>
>>>>>>>>> sequence alignment or information (older > > >
>>>>>>>>> literature, pre-genome sequencing), instead the authors
>>>>>>>>> infer
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> homology/
>>>>>>>>>>>>
>>>>>>>>>>>> sequence similarity from a Southern hybridization
>>>>>>>>>>>>
>>>>>>>>> using a MEL1
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> probe. > > > Southern analysis was listed in the old
>>>>>>>>>>>>
>>>>>>>>> ISS documentation but the
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> only > > > mention of Southerns in the new
>>>>>>>>>>>>
>>>>>>>>> documentation is under ISA in > > > conjunction with a
>>>>>>>>> sequence alignment.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> Is ISS by Southern only no longer allowed or did it
>>>>>>>>>>>>
>>>>>>>>> just get left
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> out > > > of the current documentation?
>>>>>>>>>>>>
>>>>>>>>>>>> If allowed, would I leave these annotations as ISS or
>>>>>>>>>>>>
>>>>>>>>> would it be
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> okay > > > to ISA w/ MEL1?
>>>>>>>>>>>>
>>>>>>>>>>>> thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Julie
>>>>>>>>>>>>
>>>>>>>>> ****************************************************************
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> Julie Park, Ph.D., Scientific Curator
>>>>>>>>>>>>
>>>>>>>>>>>> Saccharomyces Genome Database
>>>>>>>>>>>>
>>>>>>>>>>>> Department of Genetics
>>>>>>>>>>>>
>>>>>>>>>>>> Stanford University School of Medicine
>>>>>>>>>>>>
>>>>>>>>>>>> Stanford, CA 94305-5120 USA
>>>>>>>>>>>>
>>>>>>>>>>>> phone: (650)724-9959 fax: (650)725-1534
>>>>>>>>>>>>
>>>>>>>>>>>> http://www.yeastgenome.org
>>>>>>>>>>>>
>>>>>>>>> *****************************************************************
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>
>>>>>>>>>>>> Evidence mailing list
>>>>>>>>>>>>
>>>>>>>>>>>> Evidence at geneontology.org
>>>>>>>>>>>>
>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>
>>>>>>>>>>> Evidence mailing list
>>>>>>>>>>>
>>>>>>>>>>> Evidence at geneontology.org
>>>>>>>>>>>
>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>>
>>>>>>>>>> Evidence mailing list
>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>>
>>>>>>>>> Evidence mailing list
>>>>>>>>>
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>>>>>>>>>
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>>
>>>>>>>>> Evidence mailing list
>>>>>>>>>
>>>>>>>>> Evidence at geneontology.org
>>>>>>>>>
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>>
>>>>>>>>> Annotation mailing list
>>>>>>>>>
>>>>>>>>> Annotation at geneontology.org
>>>>>>>>>
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Do you need any additional GO annotation resources?
>>>>>>>>> Which proteins would you like annotated with GO?
>>>>>>>>>
>>>>>>>>> Let us know in the GOA User Survey, available at:
>>>>>>>>> http://www.ebi.ac.uk/GOA/contactus.html
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------
>>>>>>>>> Emily Dimmer Ph.D.
>>>>>>>>> GOA Coordinator
>>>>>>>>> EMBL-EBI
>>>>>>>>> Wellcome Trust Genome Campus
>>>>>>>>> Hinxton
>>>>>>>>> Cambridge CB10 1SD, U.K.
>>>>>>>>> Tel: +44 1223 494654
>>>>>>>>> Fax: +44 1223 494468
>>>>>>>>> email: edimmer at ebi.ac.uk
>>>>>>>>> URL: http://www.ebi.ac.uk/goa
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Evidence mailing list
>>>>>>>>> Evidence at geneontology.org
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _________________________________________________________________________
>>>>>>>>> _____________________________________________________________________
>>>>>>>>> _______________________________________________
>>>>>>>>> Annotation mailing list
>>>>>>>>> Annotation at geneontology.org
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
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