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

[Ruth Lovering]

Fair comment Chris

I have no objection to longer names

Ruth

On 14 Apr 2008, at 19:28, Chris Mungall wrote:

>
> On Apr 14, 2008, at 5:19 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
>
> Hi Ruth
>
> I agree that it's good to choose something logical, clear and  
> consistent. However, this is completely at odds with the requirement  
> to choose a unique name consisting of 3 letters.
>
> EXP is most clear, least confusing, and least open to  
> misinterpretation (maybe: perhaps many people will think  
> expression), so it's the best choice. However, we have to  
> acknowledge it's kind of daft - it's not even an acronym, as you  
> point out.
>
> I think we have to admit the current system is weird, ad-hoc,  
> broken, inconsistent, illogical and confusing. For example, nothing  
> in the letters IEA vs ISS clearly indicates the most salient  
> difference between these two codes. Yet it's impossible to change  
> them because we use them as IDs, not labels. The whole code system  
> is reminiscent of pre-GO era terminologies. I don't think GO would  
> have made much progress if we had wasted time discussing whether  
> apoptosis should be APO or APT or APS. We have a system with a  
> robust identifier lifecycle policy, synonym mechanism etc that works  
> for GO terms, why not use it for evidence too?
>
> Sticking with the system would be defensible if we knew that the set  
> of codes was stable and frozen. But this seems unlikely - there will  
> always be new experimental methods, and the subtle interactions  
> between human and computer based methods will continue to evolve.
>
> The only reason not to switch to ECO IDs immediately is the fact  
> that this requires a non-backwards compatible change. I think any  
> such change would need to be well orchestrated and would need a lead  
> time of a year, but I think it may be necessary.
>
> As a possible short term measure: what about allowing >3 letters?  
> We'd need to give a little lead time for people who have hardcoded a  
> <=3 letter assumption in software and database schemas, but this is  
> relatively trivial compared to switch to a full blown ontology. We  
> could then call EXP "EXPT". Or "EXPERIMENT". Or how about  
> "Experiment" even. So it's not a "code". Does that matter? It does  
> have the advantage of being in the same language that the majority  
> of scientists (outside the GO cognoscenti) use.
>
>> 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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>> Go mailing list
>> Go at geneontology.org
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>