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

[Mike Cherry]

Sorry if I missed the answer to this question.  A reference is  
required for EXP just like the other experimental codes.  Basically it  
has the same requirements as the experimental codes.  Thats easy for  
me to add to the filtering script.

Cheers, Mike


On Apr 10, 2008, at 6:59 AM, "Jennifer Deegan (nee Clark)" <jdeegan at ebi.ac.uk 
 > 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
>>
>>
>> _______________________________________________
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>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> -- 
> Jennifer Deegan (nee Clark)
> EMBL-European Bioinformatics Institute
> Gene Ontology Consortium
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