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

[Chris Mungall]

Changed to EXP in ECO

On Apr 14, 2008, at 9:04 AM, Jim Hu wrote:

> I agree.  And IE looks like Internet Explorer too.
>
> Jim Hu
>
> On Apr 14, 2008, at 10:58 AM, Mike Cherry wrote:
>> EXP is a much wiser name for this new code.  I strongly dislike IE,
>> too easy to confuse with IEA, plus the other experimental codes are
>> all three letters.
>>
>> -Mike
>>
>>
>> On Apr 14, 2008, at 6:53 AM, 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
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
>
>
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