[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Gwinn Giglio, Michelle
mgiglio at SOM.UMARYLAND.EDU
Fri Jun 6 09:45:12 PDT 2008
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
>>>>>>
>>>>>>> Evidence at geneontology.org
>>>>>>
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/evidence
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>>
>>>>>> Evidence mailing list
>>>>>>
>>>>>> Evidence at geneontology.org
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>>
>>>>>> 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
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
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>>>>>
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>>>>
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