[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Stacia Engel
stacia at genome.stanford.edu
Thu Jun 5 15:57:53 PDT 2008
yes, very good. the documentation also says this:
"The NAS evidence code should be used in all cases where the author
makes a statement that a curator wants to capture but for which there
are neither results presented nor a specific reference cited in the
source used to make the annotation."
see http://www.geneontology.org/GO.evidence.shtml#nas
There are results presented from a Southern hybridization, so NAS
still doesn't make sense in this case.
i'm not sure what the right answer is, but i don't think NAS is it.
stacia
On Jun 5, 2008, at 3:50 PM, 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
>>>>
>>>> > > >
>>>> *****************************************************************
>>>>
>>>> > > > _______________________________________________
>>>>
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>>>>
>>>> > > > Evidence at geneontology.org
>>>>
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>>>> evidence
>>>>
>>>> > >
>>>>
>>>> > >
>>>>
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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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>>>> 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://
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>>>> ------------------------------------------------------------------
>>>> Emily Dimmer Ph.D.
>>>> GOA Coordinator
>>>> EMBL-EBI
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridge CB10 1SD, U.K.
>>>> Tel: +44 1223 494654
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