Gramene's Rice environment ontology

Immanuel Yap noelyap at ascus.plbr.cornell.edu
Mon Oct 14 14:51:16 EDT 2002 

On Sun, Oct 13, 2002 at 03:33:34PM -0400, Pankaj Jaiswal wrote:
> 
> 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.
 
Some comments on the abiotic side:

$environment ontology ; GEO:0007359
 <abiotic environment ; GEO:0007191
  %atmospheric pressure ; GEO:0007178
  %chemical regime ; GEO:0007189
   %antibiotic regime ; GEO:0007041
   %fungicide regime ; GEO:0007268
    %benzothiadiazole ; GEO:0007267 ; synonym:BTH
   %growth hormone ; GEO:0007165
    %auxin ; GEO:0007074
     %indole acidic acid ; GEO:0007070

Synonym = IAA

    %cytokinin ; GEO:0007066
     %benzyladenine ; GEO:0007291
     %kinetin ; GEO:0007290
    %ethylene ; GEO:0007068
    %gibberellic acid ; GEO:0007069
    %jasmonic acid ; GEO:0007080

   %herbicide regime ; GEO:0007183
    %2,4-D ; GEO:0007180
    %hygromycin ; GEO:0007168

Isn't this more an antibiotic rather than an herbicide?

   %nutrient regime ; GEO:0007241
    %mineral nutrient ; GEO:0007044
     %macronutrient ; GEO:0007240
      %primary macronutrient ; GEO:0007045
       %nitrogen ; GEO:0007284
       %phosphorus ; GEO:0007397
       %potassium ; GEO:0007293
      %secondary macronutrient ; GEO:0007046
       %calcium ; GEO:0007297
       %magnesium ; GEO:0007288
       %sulphur ; GEO:0007295
     %micro nutrient ; GEO:0007239
      %boron ; GEO:0007273
      %chlorine ; GEO:0007244
      %copper ; GEO:0007261
      %iron ; GEO:0007242
      %manganese ; GEO:0007387
      %molybdenum ; GEO:0007253
      %zinc ; GEO:0007309

    %Non-mineral nutrient ; GEO:0007043
     %carbon ; GEO:0007303
     %hydrogen ; GEO:0007282
     %oxygen ; GEO:0007278

This gives the impression that a plant can use elemental/ionic carbon
and hydrogen.  [Although we use, e.g., nitrogen rather than nitrate.]

    %other nutrient ; GEO:0007047
     %aluminum ; GEO:0007306
     %chromium ; GEO:0007228
     %cobalt ; GEO:0007276

     %fertilizer regime ; GEO:0007373
      %nitrate application ; GEO:0007269

Redundant with nitrogen above?

     %fluorine ; GEO:0007225
     %iodine ; GEO:0007230
     %selenium ; GEO:0007232
     %silicon ; GEO:0007235
   %other chemical regime ; GEO:0007042
    %salicylic acid regime ; GEO:0007187
    %salt regime ; GEO:0007185
     %sodium chloride ; GEO:0007048
   %pesticide regime ; GEO:0007167

  %gaseous regime ; GEO:0007023
   %aerobic ; GEO:0007024
   %anaerobic ; GEO:0007025

I think that, for rice, the terms "aerobic" and "anaerobic" are
usually applied to soil conditions.  "Gaseous regime" sounds like
something that may be more applicable to carbon dioxide concentration
or airborne pollutants.

  %geographical region ; GEO:0007064
   %coastal region ; GEO:0007396 ; synonym:flood prone region

Plains along a river may also be flood-prone, not just coastal regions.

    %river coast region ; GEO:0007081

River mouth.

     %river delta region ; GEO:0007395 % geographical region ; GEO:0007064 % sea coast region ; GEO:0007082
    %sea coast region ; GEO:0007082
     %river delta region ; GEO:0007395 % geographical region ; GEO:0007064 % river coast region ; GEO:0007081

   %geographical region by GIS ; GEO:0007003

We don't want to be in the business of curating geographical names.  I
think we should just follow the standard names as given in a database
like the USGS Geographic Names Information System (GNIS)
http://geonames.usgs.gov/index.html

    %Africa ; GEO:0007011
    %America ; GEO:0007013

North and South America are considered to be separate continents.

     <Colombia ; GEO:0007027
     <Mexico ; GEO:0007028
     <United States of America ; GEO:0007026 ; synonym:USA
    %Asia ; GEO:0007009
     <Bangladesh ; GEO:0007035
     <Bhutan ; GEO:0007036
     <China ; GEO:0007029
     <India ; GEO:0007005
      <Bhubaneshwar ; GEO:0007017
      <Coimbatore ; GEO:0007019
      <cuttack ; GEO:0007015
      <Delhi ; GEO:0007016
      <Hissar ; GEO:0007018
     <Indonesia ; GEO:0007007
     <Japan ; GEO:0007004
     <Korea ; GEO:0007030
      <North Korea ; GEO:0007031
      <South Korea ; GEO:0007032
     <Laos ; GEO:0007038
     <Malaysia ; GEO:0007008
     <Myanmar ; GEO:0007034 ; synonym:Burma
     <Nepal ; GEO:0007037
     <Pakistan ; GEO:0007014
     <Philippines ; GEO:0007020
      <Los Banos ; GEO:0007021
     <Taiwan ; GEO:0007039
     <Thailand ; GEO:0007006
     <Vietnam ; GEO:0007033
    %Europe ; GEO:0007012
    %Oceania ; GEO:0007010
     <Australia ; GEO:0007022

Australia is a separate continent.

   %irrigated land region ; GEO:0007385

   %low land region ; GEO:0007391
    %rainfed low land region ; GEO:0007390

"lowland" is a single word (contrast with "upland")

   %river delta region ; GEO:0007395 % river coast region ; GEO:0007081 % sea coast region ; GEO:0007082

   %sahara region ; GEO:0007394 ; synonym:desert region
    %sub-sahara region ; GEO:0007393

The Sahara is the name of a specific desert (i.e., a geographic place
name).

   %tropical region ; GEO:0007061
    %sub-tropical region ; GEO:0007398

What about temperate region?

   %upland region ; GEO:0007392

  %height above sea level ; GEO:0007176

Altitude

  %light regime ; GEO:0007063
   <light intensity ; GEO:0007224
    %hight light intensity ; GEO:0007075 ; synonym:bright light
    %low light intensity ; GEO:0007271 ; synonym:shaded light
    %moderate light intensity ; GEO:0007076

   <light quality ; GEO:0007223 ; synonym:light type

Synonym = color?

    %IR light ; GEO:0007202
    %UV light ; GEO:0007222
     <UV-A ; GEO:0007002
     <UV-B ; GEO:0007001
    %visible light ; GEO:0007221
     <blue light ; GEO:0007218
     <green light ; GEO:0007217
     <indigo light ; GEO:0007219
     <orange light ; GEO:0007215
     <red light ; GEO:0007207
      %far red light ; GEO:0007203
      %near red light ; GEO:0007204
     <violet light ; GEO:0007220
     <yellow light ; GEO:0007216
   <light quantity ; GEO:0007078 ; synonym:day length ; synonym:day night length ; synonym:photoperiod
    %continuous night ; GEO:0007270 ; synonym:continuous dark light ; synonym:no light
    %long day length ; GEO:0007199
    %short day length ; GEO:0007200
  %pH ; GEO:0007171
   %acidic pH ; GEO:0007170
    %soil pH acidic ; GEO:0007059 % soil pH ; GEO:0007058
   %basic pH ; GEO:0007169
    %soil pH basic ; GEO:0007062 % soil pH ; GEO:0007058
  %soil ; GEO:0007049
   <soil fauna ; GEO:0007057
   <soil flora ; GEO:0007056
   <soil moisture ; GEO:0007055 < soil water ; GEO:0007259
   <soil pH ; GEO:0007058
    %soil pH acidic ; GEO:0007059 % acidic pH ; GEO:0007170
    %soil pH basic ; GEO:0007062 % basic pH ; GEO:0007169
   <soil texture ; GEO:0007050
    <clay ; GEO:0007054
    <organic matter ; GEO:0007052

loam?

    <sand ; GEO:0007051
    <silt ; GEO:0007053
  %temperature regime ; GEO:0007175
   %temperate ; GEO:0007172
   %temperature cold ; GEO:0007174
   %temperature normal ; GEO:0007237
   %temperature optimal ; GEO:0007238
   %termerature hot ; GEO:0007173
  %tissue/cell culture growth media ; GEO:0007266
   %liquid growth media ; GEO:0007265
    %hydroponic plant culture media ; GEO:0007067
    %suspension cell culture media ; GEO:0007071
   %solid growth media ; GEO:0007262 ; synonym:tissue culture media
  %unknown abiotic environment ; GEO:0007085
  %water ; GEO:0007198
   %humidity ; GEO:0007197
   %moisture ; GEO:0007196
   %rainfall ; GEO:0007181
   %soil water ; GEO:0007259
    <soil moisture ; GEO:0007055 < soil ; GEO:0007049
   %water regime ; GEO:0007383
  %wind ; GEO:0007382

-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org

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