GO Vs Traits

[Pankaj Jaiswal]

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
> > >
> > > --
> > -

-- 

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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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