[Go] documentation for the new 'Experimental' evidence code.

[Hannick, Linda]

I think EXP is very clear and easy for people to remember.  It gets my
vote.
-Linda

-----Original Message-----
From: go-bounces at genome.stanford.edu
[mailto:go-bounces at genome.stanford.edu] On Behalf Of Emily Dimmer
Sent: Thursday, April 10, 2008 9:25 AM
To: pgaudet at northwestern.edu
Cc: go at genome.stanford.edu
Subject: Re: [Go] documentation for the new 'Experimental' evidence
code.

...we have IC and ND!!

Emily
(I'm happy either way)

Pascale Gaudet wrote:
> Hi Emily,
>
> I like the 3 letters just because all others codes have 3 letters so 
> it seems more consistent.
>
> Pascale
>
> Emily Dimmer wrote:
>> Hi Jen,
>>
>> Thanks. Sure, I agree that 'EXP' is a very memorable code - the
reason 
>> I've put the experimental code is 'IE' is because it matches the
style 
>> of acronyms used for the other evidence codes, and that 'IE' is used
in 
>> the ECO. It would be good to hear more votes for/against on this
point.
>>
>> Emily
>>
>> Jennifer Deegan (nee Clark) wrote:
>>   
>>> Hi Emily,
>>>
>>> That looks brilliant. Very clear documentation. Was there any 
>>> objection to the idea of calling this evidence code 'EXP'? I found 
>>> that very memorable.
>>>
>>> Thanks,
>>>
>>> Jen
>>>
>>> E Dimmer wrote:
>>>
>>>     
>>>> Hi,
>>>>
>>>> Below you will find a draft of the new documentation for the 
>>>> 'Experimental' evidence code.  This draft has been passed by
evidence 
>>>> code committee. I'd be grateful if you could have a look and send
any 
>>>> comments or suggestions to me by the 18th of April so that we can 
>>>> start adding it to the GO website etc., and will mean that the code

>>>> is available for Reactome to use in their gene association file.   
>>>> The documentation of this code is quite short as it only acts to 
>>>> group each of the well-defined child experimental terms. The
acronym 
>>>> for this code is currently 'IE' - in line with the entry in the ECO

>>>> ontology.
>>>>
>>>> Thanks,
>>>> Emily
>>>>
>>>>
>>>> IE: Inferred from Experiment
>>>>
>>>> This code is used in an annotation to indicate that an experimental

>>>> assay has been located the cited reference, whose results indicate
a 
>>>> gene product's function, process involvement, or subcellular
location 
>>>> (indicated by the GO term). The IE code is the parent code for the 
>>>> IDA, IMP, IGI, IEP and IPI
>>>> experimental codes.
>>>>
>>>> The IE evidence code can be used where any of the assays described 
>>>> for the IDA, IMP, IGI, IPI or IEP evidence codes is reported.
However 
>>>> it is highly encouraged that groups should annotate to one of the 
>>>> more granular experimental codes (IDA, IMP, IGI, IPI or IEP)
instead 
>>>> of IE, and all curators directly involved in the GO Reference
Genome 
>>>> annotation effort are obliged to use these and not IE.
>>>>
>>>> The IE code exists for groups who would like to contribute 
>>>> high-quality GO annotations that are produced from directly 
>>>> associating GO terms to
>>>> gene products by citing experimental published results, but where
the 
>>>> group is unable to fit the appropriate specific experimental GO 
>>>> evidence codes to each annotation.
>>>>
>>>> ------------------------------------------------------------------
>>>>     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
>>>>    
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>       
>>
>>
>>   


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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
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
    URL:    http://www.ebi.ac.uk/goa
    

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