Plant Environment Ontology Wiki

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Unique Numberspaces for curators:

There are about 500-600 classes in this ontology.

Existing range: EO:0007001-0007634 (Gramene?)

PO-OSU: EO:0001001-0004999

Johnny Lloyd (Arabidopsis): EO:0005000- EO:0005999

Current Upper Level Hierarchy:

plant environment ontology (EO:0007403)

• abiotic environment (EO:0007191)
• biotic environment (EO:0007357)
• study type (EO:0007231)
• unknown environment (EO:0007403)

plant environment ontology (EO:0007359):

Upper level term plant environment ontology (EO:0007359) needs to be renamed and redefined.

• Current def'n:

plant environment ontology (EO:0007359): A set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.

The issue is that this definition is defining the ontology as a whole instead of defining a general plant environment.

• Revised name and def'n:

plant environment (EO:0007359): A plant treatment, growing condition, and/or study type applied to a whole plant (PO:0000003), a plant structure (PO:00090119), and/or a plant population to evaluate the plant response.

Revised comment: The Plant Environment Ontology describes the treatments, growing conditions, and/or study types used in various types of plant biology experiments. The subjects of the studies may also include in vitro plant structures (PO: PO:0000004). A plant treatment is the most specific, and may be a component of a plant growing condition. The broadest classes are the plant study types where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic treatments and different growing conditions.

plant treatment (new EO:0001001)

plant treatment (new EO:0001001): A plant environment (EO:0007359) involving the application of an abiotic or biotic treatment. (needs work)

• abiotic treatment (EO:0007191): A plant treatment (new EO:0001001) involving the application of non-biological chemical or physical factors. (needs work)
  • chemical treatment (EO:0007189): An abiotic treatment (EO:0007191) involving the application of chemical(s).(needs work)
    • inorganic chemical treatment (new EO:0001004): A chemical treatment (EO:0007189) involving the application of inorganic chemical(s).(needs work)
      • inorganic anion treatment (EO:0001009): An inorganic chemical treatment (EO:0001004) involving the application of inorganic anion(s)(CHEBI:22563).
        • sulfate treatment (new EO:0001008): An inorganic anion treatment (EO:0001009) involving the application of sulfate (CHEBI:35175).
        • phosphate treatment (new EO:0001006): An inorganic anion treatment (EO:0001009) involving the application of phosphate (ChEBI:18367).
      • inorganic cation treatment (EO:0001016):
        • ammonium treatment (EO:0001017):
      • mineral treatment (EO:0007044): An inorganic chemical treatment (EO:0001004) involving the application of a mineral or a combination of minerals (CHEBI:46662).
        • zinc treatment
        • boron treatment
        • nickel treatment (new EO:0001005): A mineral treatment (EO:0007044) involving exposure of plant to nickel (ChEBI:28112).
      • mineral salt treatment (new EO:0001007): A mineral treatment (EO:0007044) involving exposure of the plant(s) to mineral salts (CHEBI:24866). Comment: A salt (CHEBI:24866) is defined as an assembly of cations and anions. This is a general term to include the salts of various minerals.
        • organic chemical treatment (new EO:0001003): A chemical treatment (EO:0007189) involving the application of organic chemical(s).
          • carbohydrate treatment (EO:0001010): An organic chemical treatment (EO:0001003) involving the application of carbohydrate(s)(CHEBI:16646).
            • monosaccharide treatment (EO:0001011):A carbohydrate treatment (EO:0001010) involving the application of monosaccharide(s)(CHEBI:35381).
              • hexose treatment (EO:0001012): A monosaccharide treatment (EO:0001011) involving the application of hexose (CHEBI:18133) sugar(s).
                • glucose treatment (EO:0001013): A hexose treatment (EO:0001012) involving the application of glucose (CHEBI:17234).
                • fructose treatment
            • disaccharide treatment (EO:0001014): A carbohydrate treatment (EO:0001010) involving the application of disaccharide(s)(CHEBI:36233).
              • sucrose treatment (EO:0001015): A disaccharide treatment (EO:0001014) involving the application of sucrose (CHEBI:17992).
          • antibiotic treatment
          • chemical mutagen treatment
          • ethylene treatment
          • plant hormone treatment
            • salicylic acid treatment
• biotic plant treatment (EO:0007357): A plant treatment (EO:0001001) involving the application of a biotic or biological factor such as a microbe, insect, animal, or plant or a combination thereof. Need to add NCBI ids to these)
  • bacteria plant treatment (EO:0007246): A biotic plant treatment (EO:0007357) involving exposure of plant to bacteria.

physical treatment (EO:0007316)

had no definition

new def'n: An abiotic treatment (EO:0007191) involving the application of a physical factor such as gravity, wind, radiation, or a combination thereof.

• gravity treatment
• mechanical damage
• temperature treatment
• wind treatment
• radiation treatment
  • radiation quality treatment
    • gamma radiation treatment (EO:0001022): A radiation quality treatment (EO:0007154) involving the exposure to gamma radiation.

plant growth environment (EO:0001002)

New upper level class: plant growth environment (EO:0001002): A plant environment (EO:0007359) involving a combination of one or more plant treatments (EO:0001001) as well as natural conditions for plant growth.

• growth media environment (EO:0007147): A plant growth environment (EO:0001002) involving the use of growth media for growing the plants or tissue cultured samples.
  • in vitro growth media (EO:0007266) A growth media environment (EO:0007147) for in vitro culture, involving use of solid or liquid substrate and which may include nutrients.
    • in vitro liquid growth media (EO:0007265) An in vitro growth media (EO:0007265) involving use of liquid culture media as a substrate.
    • in vitro solid growth media (EO:0007262): An in vitro growth media (EO:0007266) involving use of solid growth media as a substrate.
      • agar in vitro solid growth media (new EO:0001023): An in vitro solid growth media (EO:0007262) composed of agar.
      • vertical in vitro solid growth media (new EO:0001024): An in vitro solid growth media (EO:0007266) involving use of solid growth media in a vertical orientation.

• plant nutrient environment (EO:0007241): A plant growth environment (EO:0001002) involving a plant nutrient or a combination of plant nutrients.
  • fertilizer regimen (EO:0007085): A plant nutrient environment (EO:0007241) involving the use of a fertilizer, a combination of plant nutrients.
    • chemical fertilizer regimen
    • natural fertilizer regimen
  • plant macronutrient regimen (EO:0007240):
  • primary plant macronutrient regimen (EO:0007045): A plant macronutrient regimen (EO:0007240) involving the use of the primary plant macronutrients nitrogen (N), phosphorus (P), and potassium (K).
    • nitrogen macronutrient regimen (EO:0007284): A primary plant macronutrient regimen (EO:0007045) involving the application of nitrogen.
      • urea nitrogen regimen (EO:0001025) CO(NH2)2 CHEBI:16199 A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant to urea (CHEBI:16199) as the primary or sole source of nitrogen.
      • MTA nitrogen regimen EO:0001026 5'-S-methyl-5'-thioadenosine (CHEBI:17509) A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant to5'-S-methyl-5'-thioadenosine (MTA; CHEBI:17509) as the primary or sole source of nitrogen.
      • alanine nitrogen regimen EO:0001027 alanine (CHEBI:16449) A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant to alanine (CHEBI:16449) as the primary or sole source of nitrogen.
      • glutamate nitrogen regimen EO:0001028 glutamate (CHEBI:29987) A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant toglutamate (CHEBI:29987) as the primary or sole source of nitrogen.
      • arginine nitrogen regimen EO:0001029 arginine (CHEBI:29016) A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant to arginine (CHEBI:29016) as the primary or sole source of nitrogen.
      • ornithine nitrogen regimen EO:0001030 ornithine (CHEBI:18257) A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant to ornithine (CHEBI:18257)as the primary or sole source of nitrogen.
      • glutamine nitrogen regimen EO:0001031) glutamine (CHEBI:28300) A nitrogen macronutrient regimen (EO:0007284) involving exposure of plant to glutamine (CHEBI:28300) as the primary or sole source of nitrogen.

• • plant micronutrient regimen (EO:0007239):

• gaseous environment
  • aerobic environment EO:0007024
  • anaerobic environment EO:0007025
• seasonal environment EO:0007027
• ecological environment EO:0007064

pest/pathogen/animal/plant environment (EO:0007124):

Not sure if this term is needed or if we should separate it into three terms, being pest environment, pathogen environment and animal environment. This term might no be needed however because of the children it possesses:

• pest/pathogen/animal/plant environment
  • Bacteria
  • Fungi
  • Metazoa
  • Mycoplasma
  • Stramenopiles
  • Viridiplantae
  • Virus

These seem too be self explanatory biotic environmental conditions without the use of the pest/pathogen/animal/plant environment term.

unknown environment (EO:0007403):

This term has no definition and no children, do we need it?

air temperature regimen (EO:0007161):

This term has duel parentage between temperature regimen and wind environment. This should not be a child of wind environment.

Terms without definitions:

~50 EO classes of them have no definition

EO:0007004 loam content, EO:0007051, EO:0007052, EO:0007053, EO:0007054 EO:0007075 EO:0007076 EO:0007081 EO:0007082 EO:0007089 EO:0007091 EO:0007092 EO:0007093 EO:0007156 EO:0007157 EO:0007158 EO:0007159 EO:0007193 EO:0007271 EO:0007292 EO:0007316 EO:0007373 EO:0007395 EO:0007402 EO:0007403 EO:0007404 EO:0007405 EO:0007406 EO:0007407 EO:0007408 EO:0007409 EO:0007410 EO:0007411 EO:0007610 EO:0007611 EO:0007612 EO:0007613 EO:0007614 EO:0007615 EO:0007616 EO:0007617 EO:0007618 EO:0007619 EO:0007620 EO:0007621 EO:0007622 EO:0007623 EO:0007624 EO:0007625 EO:0007626