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Draft evidence code ontology

Sue Rhee rhee at acoma.Stanford.EDU
Fri Feb 27 10:08:11 PST 2004


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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