[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?
Judith Blake
jblake at informatics.jax.org
Fri Jun 6 05:10:02 PDT 2008
TAS would work....Author says (incidently, he has a Southern result in
the paper)
judy
Stacia Engel wrote:
> 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
>>>>>
>>>>> > > >
>>>>> *****************************************************************
>>>>>
>>>>> > > > _______________________________________________
>>>>>
>>>>> > > > 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
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>>>>>
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>>>>>
>>>>> _______________________________________________
>>>>>
>>>>> Annotation mailing list
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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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>>>>>
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