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Draft evidence code ontology

Kimberly Van Auken vanauken at caltech.edu
Fri Feb 27 12:10:31 PST 2004


Michael and gofriends:

Would it be helpful to further define the IEP children to reflect what is
written in the evidence code documentation?

For example,

            @is_a at inferred from expression pattern  ;  EV:0000008
              @is_a at inferred from protein expression  ;  EV:0000010
              @is_a at inferred from transcript expression  ;  EV:0000009

might be:  

          @is_a at inferred from expression pattern  ;  EV:0000008
             @is_a at inferred from protein expression levels  ;  EV:0000010
             @is_a at inferred from transcript expression levels  ; 
 EV:0000009

Is this consistent with the intended use of the IEP evidence code?
 

The addition of the word "levels" would help to clarify when to use the IEP
codes and when to use an IDA code such as @is_a at inferred by 
immunofluorescence  ;  EV:0000007
for a given annotation.

Regards,
Kimberly


Kimberly Van Auken, PhD
Database Curator
Department of Biology, 156-29
California Institute of Technology
Pasadena, CA 91125
PHONE: (626) 395-5836
FAX: (626) 395-8611
Website: http://www.wormbase.org
email: vanauken at its.caltech.edu




Pankaj Jaiswal wrote:

>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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>>    
>>
>
>
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>
>  
>





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