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

Judith Blake jblake at informatics.jax.org
Mon Apr 14 06:50:38 PDT 2008 

I pretty much agree with Ruth
Judy

Jim Hu wrote:
> Hi everyone,
>
> Based on the discussion, I'm thinking that I won't even offer this as 
> an option on manual annotation tools on our wiki.  Should I?
>
> Jim
>
> On Apr 14, 2008, at 7:19 AM, Ruth Lovering wrote:
>> Hi Emily
>>
>> I think we need to try not to make things more confusing for the 
>> users of GO.  It would be good to choose something both logical, 
>> clear and consistent with the other evidence code acronyms. 
>>  Unfortunately there is not such an obvious acronym for 
>> the experimental code as there was for the ISS subgroups.
>>
>> From the text written for the IE code it is apparent that this code 
>> only really for non-GOC members, eg Reactome and other species 
>> specific databases.  Which may have a bearing on the decision for 
>> what acronym to choose (although maybe not).
>>
>> I would be very wary of using IE because we already have IEA and IEP 
>> and it might appear to be related to both.
>>
>> EXP has the advantage of being the most obvious acronym for 
>> experimental (and the majority of scientists will recognise it 
>> instantly as such), however breaks the usual convention of starting 
>> the acronym with 'I'.  Although as you point out not all evidence 
>> codes have 3 letters (or start with I).  I guess the RCA evidence 
>> code provides the support for the EXP acronym.  
>>
>> An alternative would be: IEX: Inferred from EXperiment
>>
>> Given the choice between IE, IEX and EXP I would favour EXP:
>>
>> EXP: inferred from EXPeriment
>>
>> With respect to the text, in the three sections the hierarchy is 
>> referred to in 3 different ways, parent, granular and specific.  So 
>> perhaps the 'specific' phrase could be used in these sections? 
>> (although this does lead to the text being rather repetitive): 
>>> 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 more specific 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 the 
>>> more specific experimental codes (IDA, IMP, IGI, IPI or IEP) instead 
>>> of the general IE code, 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.
>>
>> Finally, although the text in the ISS and IE documentation explains 
>> the hierarchy created by the new experimental codes I think it would 
>> be clearer to users if the list of evidence codes at the top of the 
>> webpage also indicated that the hierarchy exists, eg using the bullet 
>> tabs (as used for ISO etc in the supporting documentation for ISS). 
>>
>> *Curator-assigned Evidence Codes*
>> *Experimental Evidence Codes*
>> EXP: inferred from EXPeriment
>>
>>     * IDA: Inferred from Direct Assay
>>
>>     * IPI: Inferred from Physical Interaction
>>
>>     * IMP: Inferred from Mutant Phenotype
>>     * IGI: Inferred from Genetic Interaction
>>     * IEP: Inferred from Expression Pattern 
>>
>>
>> *Computational Analysis Evidence Codes*
>> ISS: Inferred from Sequence or Structural Similarity
>>
>>     * ISO: Inferred from Sequence Orthology
>>     * ISA: Inferred from Sequence Alignment
>>     * ISM: Inferred from Sequence Model
>>
>> IGC: Inferred from Genomic Context
>> RCA: inferred from Reviewed Computational Analysis 
>>
>> Ruth
>>
>>
>> On 10 Apr 2008, at 14:16, 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 <mailto:edimmer at ebi.ac.uk>
>>>>>    URL:    http://www.ebi.ac.uk/goa
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org <mailto: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 <mailto:edimmer at ebi.ac.uk>
>>>    URL:    http://www.ebi.ac.uk/goa
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
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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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