Gramene's Rice environment ontology

[Pankaj Jaiswal]

Hi Everyone,

I thought MGED has already built up some kind of an environment ontology, but
couldn't find one. So based on this presumption that there is none, I have
compiled one for Gramene, which we are considering to adopt. The first version
is available at

ftp://ftp.gramene.org/pub/gramene/ontology/environment/GR_env_ontology

There are some unresolved issues also and I need your feedback.

Pankaj
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Unresolved issues: 

like how to present the score, specifically with the abiotic environmental
factors

A score may be defined on a  

continuous scale such as for 
	growing duration in season/months/days
        day length duration in number of Hrs
        fertilizer amount applied in Kg/hectare
        pesticide amount applied in ppm or gm/lt of solution
        light spectral quality in wavelength 
        intensity in Lux etc.
        temperature in Deg C/F

Discontinuous scale

        Temp. cold/warm/hot
        application regime in terms of less (low)/more (high)/moderate
(intermediate)/normal/optimal


On this pretext what we have come up with, is that we will for the sake of
ontology use the
discontinuous scale (embedded in ontology)

such as in case of temp

cold
warm
hot
optimal
normal 


  %temperature regime ; GEO:0007123
   %temperate ; GEO:0007126
   %temperature cold ; GEO:0007124
   %temperature normal ; GRE:0007164
   %temperature optimal ; GRE:0007163
   %termerature hot ; GEO:0007125


Same is for light intensity

        light intensity high/more
        light intensity low/less
        light intensity optimal
        light intensity normal



and then if the author mentions a continuous scale, the specific info (like 13
Deg C was the temp used in trait analyses for cold tolerance) goes in the
comments section. 
I am still working on defining the discontinuous scales for each term (some are
already in).

By doing this we expect, that it gets more generic. For example in case of
different regions and
cultivars or studies for that matter (specially a comparative analyses in QTL)
these parameters on a finer level may vary, but they could still be called as
either high/low/optimal/moderate/normal.

You may have something in mind on how we can resolve this issue? In my view, if
we should bring the scoring attributes in the environment ontology, otherwise it
is as good as a free text.


Lincoln Stein wrote:
> 
> It looks very promising.  What are the major unresolved issues?
> 
> 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   
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