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Draft evidence code ontology

Tanya Berardini tberardi at acoma.Stanford.EDU
Fri Feb 27 11:59:56 PST 2004


My intention is put up an ontology of _only_ the evidence descriptions
that we use here at TAIR and not attempt to cover every possible
experiment/evidence that could be used.  Our descriptions have been pretty
stable for the past year or so, with only minimal additions/changes to
these existing entries.  Not all of them correspond to experiments.  Sue
and I will work on providing definitions for all of these descriptions
before putting it up on OBO in the not too distant future.

We're putting it up so that others can have a look at what we have been
successful in implementing and using at TAIR for the past couple of years
and provide some food for thought for other databases that might want to
do similar things.

Tanya

On Fri, 27 Feb 2004, 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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-------------------------------------------------------------------------------
Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------


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