GO Vs Traits
Pankaj Jaiswal
pj37 at cornell.edu
Tue Sep 11 09:06:41 EDT 2001
leonore,
your comments are right, we need those terms. As a trait "elongation" is
referred as "Elongation ability". therefore i have reframed it for "Elongation
ability" under the traits. That is how the breeders and Susan suggested me.
I am going through the photosynthesis, realted terms these days and will get
back to you when i compile them.
Yesterday, i have sent my trait ontology files to be put up on the CVS server. I
hope it will be up soon. BTW sdid you send all teh info Lincoln wanted with ref.
to CVS facility.
thanks
pankaj
Leonore Reiser wrote:
>
> Pankaj- a few comments about elongation as a process
>
> - will add cell elongation as a cellular process- in the works.
> -a process might be internode elongation as a developmental process.
> Leonore
>
> On Fri, 7 Sep 2001, Pankaj Jaiswal wrote:
>
> > Ni,
> >
> > I have the comments as follows:###
> >
> > Jun Jian Ni wrote:
> > >
> > > Hi,
> > >
> > > I have three points.
> > >
> > > 1. photoperiod sensitivity is not light stress related trait. It is related with
> > > maturity and also called as "environmental related trait". However, it is not related
> > > stress.
> >
> > ### I will call it a light related since it represents the affect on plant due
> > to Day length period. Now this change in day length period, is one of the
> > component which affect the maturity of plant in terms of "Days to
> > heading/flowering /maturity" i.e either there is a delay /early flowering.
> >
> > > 2. Kneeling ability and submergence tolerance and elongation ability are traits. So, no
> > > need put "trait" after those again and again.
> > >
> >
> > ### Accepted, but have a look at Michael's e mail , he suggests that elongation
> > is a biological process.
> >
> > > 3. I suggest to remove "physicochemical stress ", " chemical stress " and
> > > "physiological stress". We can directly use "response to water stress" "response to
> > > temperature stress", etc.
> >
> > ### Again try to resolve, response is a process/trait. I have changed the above
> > terms as broad trait categories.
> >
> >
> > ### Here comes the contradiction between the Molecular biologist/Biochemist and
> > the plant breeder/Geneticist, on how he percieves the response. Whether as a
> > trait or as a Bilogical process ??
> >
> > pankaj
> >
> > >
> > > Ni
> > >
> > > Pankaj Jaiswal wrote:
> > >
> > > > Wait wait,
> > > >
> > > > let me rephrase the things here. What actually Michael did here and I can do the
> > > > same too. (i apologise for not doing it earlier).....
> > > > in trait ontologies, instead of framing the term as "deep water stress" , which
> > > > is rightly pointed out by Midori and Micheal as physiological stress type.
> > > > Michael reframed it as "response to deep water" which then becomes the
> > > > biological process. Now what? if I reframe it as
> > > >
> > > > "deep water related trait"
> > > >
> > > > then will it fit the traits ontology. This is to curate a group of defined
> > > > classes of trait factors (on a higher note) which the people will be looking in
> > > > for. They later become the parent for X-tolerance/X-resistance type of trait,
> > > > otherwise the higher nodes of biotic/abiotic stress related traits will have a
> > > > long list of children.
> > > >
> > > > > These, as Midori says, are environmental conditions:
> > > > >
> > > > > %physicochemical stress ; GO:0301797
> > > > > %chemical stress ; GO:0301774
> > > > > %physiological stress ; GO:0301775
> > > > > %deepwater stress ; GO:0302189 ; synonym:flooding
> > > > > %drought stress ; GO:0302193
> > > > > %light stress ; GO:0301777
> > > > > %temperature stress ; GO:0302206
> > > >
> > > > I change them to :
> > > >
> > > >
> > > > > %physicochemical stress related trait ; GO:0301797
> > > > > %chemical stress related trait; GO:0301774
> > > > > %physiological stress related trait; GO:0301775
> > > > > %deepwater stress related trait; GO:0302189 ; synonym:flooding related trait
> > > > %kneeling ability trait ; GO:0302185 ; ICIS:1212 ; synonym:KnA
> > > > %submergence tolerance trait; GO:0302187 ; ICIS:1215 ; synonym:Sub
> > > > %elongation trait; GO:0302188 ; ICIS:1209 ; synonym:Elon
> > > > > %drought stress related trait; GO:0302193
> > > > %drought sensitivity ; GO:0302192 ; synonym:DRS
> > > > %drought tolerance ; GO:0302191
> > > > %drought recovery ; GO:0302190 ; synonym:DRR
> > > > > %light stress related trait; GO:0301777
> > > > %photoperiod sensitivity ; GO:0301776
> > > > > %temperature stress related trait; GO:0302206
> > > > %cold tolerance ; GO:0302204 ; synonym:CTol
> > > > %heat tolerance ; GO:0302194 ; ICIS:1210 ; synonym:HTol
> > > >
> > > >
> > > > pankaj
> > > >
> > > > Lincoln Stein wrote:
> > > > >
> > > > > > %response to deepwater stress ; GO:0302189 ; synonym:flooding
> > > > >
> > > > > "synonym: response to flooding" no?
> > > > >
> > > > > Lincoln
> > > > >
> > > > > --
> > > > -
> >
> > --
> >
> > **************************************************************
> > 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
> > **************************************************************
> >
> >
>
> -------------------------------------------------------------------------------
> 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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