[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Karen Christie
kchris at genome.stanford.edu
Thu Jun 5 13:53:45 PDT 2008
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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> > >
>
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>
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> Emily Dimmer Ph.D.
> GOA Coordinator
> EMBL-EBI
> Wellcome Trust Genome Campus
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> Cambridge CB10 1SD, U.K.
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