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Draft evidence code ontology

Pankaj Jaiswal pj37 at cornell.edu
Fri Feb 27 11:46:35 PST 2004


I think what we are getting here is a big list of experiments/analyses
types and I presume it is going to be the same as an ontology of
experiments avilable from TAIR.

Pankaj


> Michael,
>
> I strongly urge you to define the terms before you put the ontology in
> OBO.
>
> Thanks,
> Sue
>
> On Fri, 27 Feb 2004, Michael Ashburner (Genetics) wrote:
>
>> Thanks for the input. I have - I hope - taken account of the
>> suggestions.
>>
>> 1. Now always 'inferred from', except 'inferred by curator'
>> 2. ISS corrected
>> 3.     @is_a at inferred from overexpression ; EV:0000016
>>   removed
>> 4. Becky: 'There are several evidence codes under 'inferred from direct
>> assay',
>> which I think should not be, and should be
>> moved up a level.
>> inferred from genetic interaction
>> inferred from mutant phenotype
>> inferred sequence similarity
>> inferred from expression pattern'
>>
>> Midori made the same point.
>> .. I disagree, these are all direct assays
>>
>> 5: Becky: 5. 'inferred from protein binding ; EV:0000024' and 'inferred
>> from
>> ligand binding ; EV:0000023' sound very broad.
>> Since we already have inferred from co-purification and inferred from
>> 2-hybrid
>> interaction, do we need EV:0000023 and
>> EV:0000024?
>>
>> .. yes ligand is broader than protein, could be a calcium-binding assay
>> for
>> example
>>
>> 6: Becky: 6. I think it may be nice to have a general 'inferred from
>> experiment'
>> evidence code for all the IDA, IPI, IGI, IEP
>> and IMPs?
>> .. I think IDA _is_ inferred from experiment
>>
>> 7: Gillian: would this apply to both loss of function and gain of
>> function
>> mutants
>> made eg. by EMS, X ray etc. i.e. any non-transgenic mutation made in an
>> organism ? or just loss of function, to contrast with "inferred from
>> ectopic expression"
>>
>> . have added
>>
>>     @is_a at inferred from loss-of-function mutant phenotype ; EV:0000016
>>     @is_a at inferred from gain-of-function mutant phenotype ; EV:0000042
>>
>> >From David S: 1. Should 2 hybrid and protein binding be under ligand
>> binding?
>>
>> .. yes, I think so.
>>
>> 8. From David S: 2. The subdivision of IGI seems a bit odd.  Would
>> enhancement
>> and suppression
>>
>> .. yes I agree, changed, now:
>>
>>    @is_a at inferred from genetic interaction ; EV:0000011 ; synonym:IGI
>>    @is_a at inferred from functional complementation ; EV:0000012
>>     @is_a at inferred from transgenic rescue ; EV:0000013
>>     @is_a at inferred from transient rescue ; EV:0000038
>>
>> 9. From David S: 3. I may be being pedantic, but should sequence
>> similarity and
>> its children be
>>
>> I have created a new parent
>>
>>  @is_a at inferred from in-silico analysis ; EV:0000043
>>
>> with
>>   @is_a at inferred from electronic annotation ; EV:0000036 ; synonym:IEA
>>    @is_a at inferred from sequence or structural similarity ; EV:0000041 ;
>> synonym:ISS @is_a@ inferred from in-silico analysis ; EV:0000043
>>
>> as kids
>>
>>
>>
>> Updates attached in GO f/file and obo formats.
>>
>> Michael
>>
>>
>
> -----------------------------------------------------------------------------
> Sue Rhee                         	rhee at acoma.stanford.edu
> The Arabidopsis Information Resource	URL: www.arabidopsis.org
> Carnegie Institution of Washington	FAX: +1-650-325-6857
> Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> -----------------------------------------------------------------------------
>
>
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