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

[Michael Ashburner]

Mine to, EXP it should be.
M
On 14 Apr 2008, at 09:53, Hannick, Linda wrote:

> 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
>>>>>
>>>
>>>
>>>
>
>
> -- 
>
>
> 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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