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Draft evidence code ontology

Harold Drabkin hjd at informatics.jax.org
Fri Feb 27 07:39:38 PST 2004


Hi all

I have a problem with an ISS being thought of as a type of IDA or
experiment. It is very important to make a distinction between something
with experiments behind them.
For example, suppose two proteins are similar except for one amino acid, and
the identity of the amino acid determines whether or not the protein
functions as a kinase.
ISS would predict that one was a kinase based on similarity to the other,
but the real experiment (IDA) would demonstrate that one did NOT have kinase
activity.

hjd

On 2/27/04 6:13 AM, "David Sutherland" <djs93 at gen.cam.ac.uk> wrote:

> 
> Hi Michael,
> 
> Here's my penneth:
> 1. Should 2 hybrid and protein binding be under ligand binding?
> 
> 2. The subdivision of IGI seems a bit odd.  Would enhancement and suppression
> better terms than rescue?  To use rescue seems at odds with FlyBase phenotype
> curation, (where as you know it is currently reserved for suppression of a
> phenotype by alleles/transgenes of the same gene).  The same argument could
> apply to functional complementation - currently in use by FlyBase for cross
> species rescue by "homologues".  Functional complementation in this sense is
> clearly a useful form of evidence for assigning GO terms, but it seems quite
> distinct from the usual usage of 'genetic interaction'.
> 
> 
> 3. I may be being pedantic, but should sequence similarity and its children be
> under 'inferred from direct assay'?  I guess one could consider them in silico
> assays (?).
> 
> Dave
> 
>> Envelope-to: djs93 at gen.cam.ac.uk
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>> From: "Michael Ashburner (Genetics)" <ma11 at gen.cam.ac.uk>
>> Subject: Draft evidence code ontology
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>> 
>> 
>> 
>> Folks - here is a very drafty evidence codes ontology (w/out definitions).
>> Feedback please on all of its particulars.
>> 
>> Michael
>> 
>> !autogenerated-by:     DAG-Edit version 1.409-beta-4
>> !saved-by:             ma11
>> !date:                 Thu Feb 26 17:10:28 GMT 2004
>> !version: $Revision: 1.23 $
>> !type: @is_a@ is_a is a
>> $Evidence_Codes_Ontology ; EV:0000000
>>  @is_a at inferred by curator ; EV:0000001 ; synonym:IC
>>  @is_a at inferred by electronic annotation ; EV:0000036 ; synonym:IEA
>>  @is_a at no biological data ; EV:0000035 ; synonym:ND
>>  @is_a at non-traceable author statement ; EV:0000034 ; synonym:NAS
>>  @is_a at not_recorded ; EV:0000037 ; synonym:NR
>>  @is_a at traceable author statement ; EV:0000033 ; synonym:TAS
>>   @is_a at inferred from direct assay ; EV:0000002 ; synonym:IDA
>>    @is_a at inferred by cell fractionation ; EV:0000004
>>    @is_a at inferred by immunofluorescence ; EV:0000007
>>    @is_a at inferred by physical interaction ; EV:0000021 ; synonym:IPI
>>     @is_a at inferred from co-purification ; EV:0000022
>>     @is_a at inferred from ligand binding ; EV:0000023
>>      @is_a at inferred from 2-hybrid interaction ; EV:0000025
>>      @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred by
> protein 
>> assay ; EV:0000039
>>    @is_a at inferred by protein assay ; EV:0000039
>>     @is_a at inferred by enzyme assay ; EV:0000005
>>     @is_a at inferred by immunological assay ; EV:0000040
>>     @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from
> ligand 
>> binding ; EV:0000023
>>    @is_a at inferred by reconstitution assay ; EV:0000003
>>    @is_a at inferred from expression pattern ; EV:0000008 ; synonym:IEP
>>     @is_a at inferred from protein expression ; EV:0000010
>>     @is_a at inferred from transcript expression ; EV:0000009
>>    @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
>>    @is_a at inferred from mutant phenotype ; EV:0000014 ; synonym:IMP
>>     @is_a at inferred from anti-sense experiment ; EV:0000018
>>     @is_a at inferred from ectopic expression ; EV:0000017
>>     @is_a at inferred from gene mutation ; EV:0000015
>>     @is_a at inferred from overexpression ; EV:0000016
>>     @is_a at inferred from RNAi experiment ; EV:0000019
>>    @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@
>> inferred 
>> sequence similarity ; EV:0000041
>>    @is_a at inferred from specific protein inhibition ; EV:0000020
>>    @is_a at inferred sequence similarity ; EV:0000041 ; synonym:ISS
>>     @is_a at inferred from curated BLAST match ; EV:0000030
>>      @is_a at inferred from curated BLAST match to nucleic acid ; EV:0000032
>>      @is_a at inferred from curated BLAST match to protein ; EV:0000031
>>     @is_a at inferred from motif similarity ; EV:0000028
>>      @is_a at inferred from InterPro motif similarity ; EV:0000029
>>     @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@
> inferred 
>> from direct assay ; EV:0000002
>>     @is_a at inferred from structural similarity ; EV:0000027
>> 
>> 
>> 
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> 
> 
> 
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