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

[Chris Mungall]

At what point do we consider moving to the numeric meaning-free  
identifers used in ECO?

Obviously not a decision to be taken lightly since all assoc parsers  
would need to be rewritten. But there would be advantages



On Apr 10, 2008, at 7:05 AM, Valerie Wood wrote:

>
>
> I prefer EXP.
> IE coulod be confused with  IEA
>
> Val
>
> Emily Dimmer <edimmer at ebi.ac.uk> wrote:
>> ...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
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
>
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