[Go] documentation for the new 'Experimental' evidence code.
Jim Hu
jimhu at tamu.edu
Mon Apr 14 06:33:06 PDT 2008
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
>>>> 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
=====================================
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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