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

[Emily Dimmer]

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
>


-- 


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