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

[Jim Hu]

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
>>
>>
>> _______________________________________________
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>> http://fafner.stanford.edu/mailman/listinfo/go
>>
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>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> _______________________________________________
> Go mailing list
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=====================================
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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