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Draft evidence code ontology

Rebecca Foulger ref26 at gen.cam.ac.uk
Fri Feb 27 02:26:11 PST 2004



Michael etc, 

My comments:

1. I think it should be consistent between 'inferred from' and 'inferred by'. On the GO web page at the moment it's 
'inferred from' so I think we should go with this.

2. inferred sequence similarity ; EV:0000041 should be inferred from sequence or structural similarity ; EV:0000041.

3. inferred from ectopic expression and inferred from overexpression. I think there is quite a bit of overlap between 
these 2. Do we need two separate evidence codes?

4. 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

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?

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?

Thanks,
Becky


> Date: Thu, 26 Feb 2004 18:14:42 +0000 (GMT)
> From: "Michael Ashburner (Genetics)" <ma11 at gen.cam.ac.uk>
> Subject: Draft evidence code ontology
> To: gofriends at genome.stanford.edu 
> 
> 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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