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Draft evidence code ontology

Anand Kumar anand.kumar at ifomis.uni-leipzig.de
Fri Feb 27 06:50:38 PST 2004


One small suggestion.
For each of these terms, there should be an ontology after you remove "inferred
from". That way one would be able to justify the constitutional nature of GO
terms, that, the large terms are derived from the smaller terms.
Based on that, maybe some of the hierarchy mentioned in the email threads will
change too.
For example, you will clearly see some changes if you remove "inferred from".
Will you put "genetic interaction" and "mutant phenotype" together in the same
ontology? Or will you call is "mutant phenotype expression", since both should
be functions or both should be substances?
If you do this small exercise, some of the changes needed would become more
obvious.

Have a good weekend.
Anand.

> 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
> 
> 
-- 
Anand Kumar
IFOMIS
University of Leipzig
Härtelstraße 16-18
04107 Leipzig
Germany
http://www.uni-leipzig.de/~akumar/
http://labmedinfo.org/people/cv/kumar.htm


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