[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Susan Tweedie
sart2 at gen.cam.ac.uk
Fri Jun 6 10:18:37 PDT 2008
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
> >>>>>>
> >>>>>>> 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
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>>
> >>>>>> 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
> >>>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> _______________________________________________
> >>>>> Annotation mailing list
> >>>>> Annotation at geneontology.org
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> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Annotation mailing list
> >>>>> Annotation at geneontology.org
> >>>>> http://fafner.stanford.edu/mailman/listinfo/annotation
> >>>>
> >>> _______________________________________________
> >>> 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
>
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