[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Stacia Engel
stacia at genome.stanford.edu
Thu Jun 5 15:44:26 PDT 2008
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
> >
> > > > >
> *****************************************************************
> >
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> >
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> >
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> >
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> evidence
> >
> > > >
> >
> > > >
> >
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> >
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> >
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> >
> > >
> >
> > >
> >
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> >
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> >
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> >
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> >
> >
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> >
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> >
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> >
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> >
> >
> >
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> >
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> >
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> >
> >
> > --
> >
> >
> > 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
> >
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