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

Mon Apr 14 05:19:08 PDT 2008

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
>>>    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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