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Draft evidence code ontology

Bruskiewich, Richard (IRRI) r.bruskiewich at cgiar.org
Sun Feb 29 16:23:20 PST 2004


Echoing sentiments expressed elsewhere, maybe it is sensible to keep the
original GOC evidence codes simply and give this second set of
"experiment/analysis" types separate billing as an ontology, then do the
cross product, as individual groups see fit?

Cheers,
Richard 

PS. Hi everybody... Now that I've been annointed "informatics network task
leader" (which essentially means "ontology, XML and web services
development") for the Genetic Resources Challenge Program  that I told you
folks about in Stanford (see www.genesforcrops.org), I anticipate becoming
more actively involved in the consortium with some of my staff and scholars
in tow.  

-----Original Message-----
From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] 
Sent: Saturday, February 28, 2004 3:47 AM
To: Sue Rhee
Cc: Michael Ashburner; gofriends at genome.stanford.edu; ref26 at gen.cam.ac.uk
Subject: Re: Draft evidence code ontology

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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