possible changes in process for 'traity terms' (was GO Vs Traits)

[Leonore Reiser]

Pankaj- thanks for the suggestions. I need some clarifiation though


>
> May be you would like to include/reconfigure

I am not sure what you are suggesting to reconfigure
do you mean : change blue light response -> response to blue light?

or do you mean reconfigure the structure as below?
see comments..##

> %response to light (GO:0009416)
>  %response to light quality type (depends on the wavelength)
>   %perception of light (GO:0009583)
>   %blue light response (GO:0009637)
>   %red/far-red light response (GO:0009639)
>   %UV response (GO:0009411)
>  %response to light intensity (GO:0009642)(eg: response to shade/open light, its
> trivial but people do use this term, more or less depends on the light enery)
##NOT sure what you are getting at with the above term (which one is 'this
term') there are terms for: %response to high light intensity ; GO:0009644
and %response to low light intensity ; GO:0009645 and %shade avoidance ;
GO:0009641.

>   %photoinhibition (related with photosynthesis also)
>   %photoreduction
>  %response to photoperiod (GO:0009648) ; synonym: photoperiodism ; synonym:
> response to duration of light



>
> others to be included are
> %photoemission
> %photoexcitation
> %photokinesis
> %photolysis
> %photoinactivation

Want to suggest some definitions for these terms?

>
> you will need to look at the
>
> UV protection (GO:0009650) ???

currently:
    %light response ; GO:0009416
      %UV protection ; GO:0009650
      %UV response ; GO:0009411

change to

	%response to UV ; GO:0009411
	 %UV protection ; GO:0009650

?
Leonore

> i will be coming up with more terms on this later.
>
> pankaj
>
> Leonore Reiser wrote:
> >
> > Hi- a few thoughts for comment.
> >
> > Regarding Pankaj's comments about traits and process, and considering
> > Michael and Midori
> > and Lincoln's comments.
> >
> > 1. remove disease resistance (GO:0009614) and replace with
> >
> > response to pathogen (incompatible interaction)
> >
> > def: a response of an organism to a pathogenic agent that
> > that prevents the occurance or spread of disease.
> >
> > then make similar changes to
> >
> > resistance to pathogenic fungi GO:0009619
> > resistance to pathogenic bacteria GO:0009622
> > resistance to pathogenic protozoa GO:0001564
> >
> > 2. remove drought tolerance GO:0009633.
> >  also remove freezing tolerance GO:0009632 on the same basis
> >
> > 3. Change the wording of things like
> >  cold response GO:0009409 to response to cold
> >
> > def: a change in state or activity of an organism (in terms of movement,
> > secretion, changes in gene expression, enzyme production, etc..) as a
> > result of exposure to temperatures below the optimal range for that
> > organism
> >
> >  and similarly change
> > heat response GO: 0009408 to response to heat
> >
> > def: a change in state or activity of an organism (in terms of movement,
> > secretion, changes in gene expression, enzyme production, etc..) as a
> > result of exposure to temperatures above the optimal range for that
> > organism
> >
> > 4.
> > %flooding response ; GO:0009413  already exists , could change the string
> > for consistancy to response to flooding...
> >
> > >
> > > >  >       %response to deepwater stress ; GO:0302189 ; synonym:flooding
> > > >
> > > > "synonym: response to flooding" no?
> >
> > 5. add drought recovery
> >
> > def?:a change in state or activity of an organism (in terms of movement,
> > secretion, changes in gene expression, enzyme production, etc..) as a
> > result of prolonged deprivation of water that results in a return to a
> > normal (non-stressed) state.
> >
> > 6. Elongation as a process is just awaiting me getting it together to send
> > out a new set of terms (prompted by expansins) for cell elongation and
> > related terms (e.g. wall loosening...). I
> > assume that elongation in response to flooding refers to cell
> > elongation in the internodes -yes ( which can be measured as an increase
> > in height).
> >
> > Thanks in advance for feedback.
> >
> > Leonore
> > -------------------------------------------------------------------------------
> > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology             URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------------
>
> --
>
> **************************************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org   http://ars-genome.cornell.edu/rice
> **************************************************************
>

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Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
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