Latest revision as of 20:59, 8 December 2014

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 - has not been used yet

Revisions to Upper Level Hierarchy:

Formerly:
- 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: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 plant treatment (EO:0007191) involving the application of chemical(s).(needs work)
  - chemical stress treatment (EO:0001036): A chemical treatment (EO:0007189) that induces stress.
    - oxidative stress treatment (EO:0001037): A chemical stress treatment (EO:0001036) involving use of oxidative stress-inducing chemicals.
    - osmotic stress treatment (EO:0001038): A chemical stress treatment (EO:0001036) involving use of osmotic stress-inducing chemicals.
    - chemical mutagen treatment (EO:0007149): A chemical stress treatment (EO:0001036) involving use of mutagen for the mutagenesis process.
  - inorganic chemical treatment (new EO:0001004): A chemical treatment (EO:0007189) involving the application of inorganic chemical(s).(needs work)
    - inorganic gas treatment (EO:0001055): An inorganic chemical treatment (EO:0001004) involving the application of a gas or mixture of gases.
      - carbon dioxide treatment (EO:0001020): An inorganic gas treatment (EO:EO:0001055) that involves the application of carbon dioxide (CHEBI:16526).
        elevated carbon dioxide treatment (EO:0001056): A carbon dioxide treatment (EO:0001020) involving the manipulation of increasing the carbon dioxide (CHEBI:16526) concentration.
    - 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).
        limited sulfate treatment (EO:0001045): A sulfate treatment (EO:0001008) involving exposure to limiting amounts or the absence of sulfate (CHEBI:35175).
      - phosphate treatment (new EO:0001006): An inorganic anion treatment (EO:0001009) involving the application of phosphate (ChEBI:18367).
        limited phosphate treatment (EO:0001046): A phosphate treatment (EO:0001006) involving exposure to limiting amounts or absence 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).
      - 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).
        limited glucose treatment (EO:0001043): A glucose treatment (EO:0001013) involving exposure to limiting amounts or the absence of glucose (CHEBI:17234).
        
        fructose treatment -not added yet
        
        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).
        
        salicylic acid treatment
        
        methyl jasmonate treatment (EO:0007407)
        
        5-methyltryptophan treatment (EO:0007408)
        
        cadmium chloride (EO:0007223)
        
        ethylene treatment
        
        antibiotic treatment
        
        chemical mutagen treatment (EO:0007149)
        
        plant hormone treatment

biotic plant 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.
- fungal plant treatment EO:0007233 A biotic plant treatment (EO:0007357) involving exposure of a plant to a fungus or a combination of fungi.
- Viridiplantae plant treatment EO:0007005 : A biotic plant treatment (EO:0007357) involving exposure of a plant to another plant. Moved much of the existing def'n to the comment: "Suggests the exposure of plant to other plants found in its growth environment. These plants may be growing as a weed or as part of normal farming practices. This treatmnet is part of an assay of any direct or indirect, harmful or beneficial effect of one plant on another through the production of chemical compounds (allelochemicals) that escape in the environment. Viridiplantae include all plants from algae through angiosperms."
- virus plant treatment (EO:0007210): A biotic plant treatment (EO:0007357) involving exposure of a plant to a virus or a combination of two or more viruses.
- metazoan plant treatment (EO:0007349): A biotic plant treatment (EO:0007357) involving exposure of a plant to a metazoan organism (animal).
  - insect plant treatment(EO:0007333): A metazoan plant treatment (EO:0007349) involving exposure of a plant to an insect or a mixture of insects.
    - Hymenoptera insect plant treatment (EO:0001032): An insect plant treatment (EO:0007333) involving the exposure of a plant to an insect(s) of the Hymenoptera order.
      - parasitic wasp insect plant treatment (EO:0001033): A Hymenoptera insect plant treatment (EO:0001032) that involves exposure to parasitic wasps.
- bacterial plant treatment (EO:0007246) A biotic plant treatment (EO:0007357) involving exposure of a plant to bacteria.
  - Obsoleted: Proteobacterial plant treatment (EO:0007108)
  - Erwinia bacterial plant treatment (EO:0007143): A bacterial plant treatment (EO:0007246) involving the exposure to bacteria of the genus Erwinia.
  - Xanthomonas bacterial plant treatment (EO:0007145): A bacterial plant treatment (EO:0007246) involving the exposure to bacteria of the genus Xanthomonas.
  - Pseudomonas bacterial plant treatment (EO:0007144): A bacterial plant treatment (EO:0007246) involving the exposure to bacteria of the genus Pseudomonas.
    - Pseudomonas syringae plant treatment(new EO:0001034): A Pseudomonas plant treatment (EO:0007144) involving the exposure to bacteria of the Pseudomonas syringae group.

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 mutagen treatment (EO:0001039): A radiation treatment (EO:0007151) involving exposure of plant to chemicals or radiation resulting in perturbations to the genome.
- radiation intensity regimen
  - light intensity regimen
    - light-induced photooxidative stress treatment (EO:0001040): A light intensity regimen (EO:0007224) involving use of light-dependent generations of reactive oxygen species.
- 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 medium environment (EO:0007147): A plant growth environment (EO:0001002) involving the use of a growth medium for growing plants or tissue cultured samples.
- in vitro growth medium (EO:0007266): A growth medium environment (EO:0007147) for in vitro culture, involving use of a solid or liquid substrate and which may include nutrients and other amendments.
  - in vitro liquid growth medium (EO:0007265): An in vitro growth medium (EO:0007265) involving use of liquid culture media as a substrate.
  - in vitro solid growth medium (EO:0007262): An in vitro growth medium (EO:0007266) involving use of a solid growth medium as a substrate.
    - agar growth medium (EO:0001023): An in vitro solid growth medium (EO:0007262) composed of agar.
    - vertical agar growth medium (EO:0001024): An agar growth medium (EO:0001023) 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.
- non-mineral nutrient regimen (EO:0007043): Treatment involving the exposure of plant to molecular forms of nutrient as supplement to study various types of responses.
  - carbon nutrient regimen (EO:0007303): The treatment involving exposure of plant to carbon source as supplement to study various types of responses.
    - limited carbon regimen (EO:0001044): A carbon nutrient regimen (EO:0007303) involving exposure to limiting amounts or the absence of carbon (CHEBI:27594).
- fertilizer regimen (EO:0007085): A plant nutrient environment (EO:0007241) involving the use of a fertilizer, a combination of plant nutrients.
  - chemical fertilizer regimen
    - nitrogen fertilizer regimen (EO:0007102)
      - nitrate regimen (EO:0007406)
        limited nitrate regimen (EO:0001054): A nitrate regimen (EO:0007406) involving exposure to limiting amounts or the absence of nitrate (CHEBI:17632).
  - 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.
      - limited nitrogen regimen (EO:0001050): A nitrogen macronutrient regimen (EO:0007284) involving exposure to limiting amounts or the absence of nitrogen (CHEBI:25555).
      - 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.
    - potassium nutrient regimen (EO:0007293): The treatment involving exposure of plant to macronutrient potassium as supplement to study various types of responses.
      - limited potassium regimen (EO:0001051): A potassium nutrient regimen (EO:0007293) involving exposure to limiting amounts or the absence of potassium (CHEBI:26216).
  - secondary macronutrient (EO:0007046): Treatment involving the use of macronutrients (Ca, Mg, S) as supplement to study various types of responses. These macronutrients are used less often as fertilizers than the primary elements.
    - magnesium nutrient regimen (EO:0007288): The treatment involving exposure of plant to macronutrient magnesium as supplement to study various types of responses.
      - limited magnesium regimen (EO:0001049): A magnesium nutrient regimen (EO:0007288) involving exposure to limiting amounts or the absence of magnesium (CHEBI:25107).
    - sulfur nutrient regimen (EO:0007295): The treatment involving exposure of plant to macronutrient sulfur as supplement to study various types of responses.
      - limited sulfur regimen (EO:0001052): A sulfur nutrient regimen (EO:0007295) involving exposure to limiting amounts or the absence of sulfur (CHEBI:26833).

- plant micronutrient regimen (EO:0007239):
  - zinc nutrient regimen (EO:0007309): The treatment involving exposure of plant to micronutrient zinc as supplement to study various types of responses.
    - limited zinc treatment (EO:0001041): A zinc nutrient treatment (EO:0007309) involving exposure to limiting amounts or absence of zinc (CHEBI:27363).
  - boron nutrient regimen (EO:0007273): The treatment involving exposure of plant to micronutrient boron as supplement to study various types of responses.
    - limited boron treatment (EO:0001042): A boron nutrient regimen (EO:0007273) involving exposure to limiting amounts or absence of boron (CHEBI:27560).
  - iron nutrient regimen (EO:0007242):The treatment involving exposure of plant to micronutrient iron as supplement to study various types of responses.
    - limited iron regimen (EO:0001047): An iron nutrient regimen (EO:0007242) involving exposure to limiting amounts or the absence of iron (CHEBI:18248).
  - molybdenum nutrient regimen (EO:0007253): The treatment involving exposure of plant to micronutrient molybdenum as supplement to study various types of responses.
    - limited molybdenum regimen (EO:0001048): A molybdenum nutrient regimen (EO:0007253) involving exposure to limiting amounts or the absence of molybdenum (CHEBI:28685).
  - manganese nutrient regimen (EO:0007387): The treatment involving exposure of plant to micronutrient manganese as supplement to study various types of responses.
    - limited manganese regimen (EO:0001053): A manganese nutrient regimen (EO:0007387) involving exposure to limiting amounts or the absence of manganese (CHEBI:18291).

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

plant study type (EO:0007231)

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: plant treatment (EO:0001001) branch:

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

child terms of radiation treatment (EO:0007151) >> radiation intensity regimen (EO:0007152) >> light intensity regimen (EO:0007224)

high light intensity regimen (EO:0007075):
moderate light intensity regimen (EO:0007076):
day light intensity EO:0007193
low light intensity regimen EO:0007271

Child terms of radiation treatment (EO:0007151) >> radiation quality treatment (EO:0007154):

3-H (EO:0007610):
3-H-deoxycytidine (EO:0007611):
3-H-thymidine (EO:0007612):
32-P (EO:0007613):
agr ray (EO:0007614):
Bevatron irradiation (EO:0007615):
deuteron irradiation (EO:0007616):
ggr ray (EO:0007617):
- 137-Cs or ggr ray (EO:0007618):
- 226-Ra or agr ray (EO:0007619):
- 60-Co or ggr ray (EO:0007620):
magnetic field (EO:0007621):
neutrons (EO:0007622):
- 252-Cf fission neutrons (EO:0007623):
radio wave (EO:0007624):
stratosphere exposure (EO:0007625):
supersonic-treatment (EO:0007626):

children of chemical treatment (EO:0007189)

CCP (EO:0007292): A herbicide regimen (EO:0007183) which involves the...
brassinosteroid (EO:0007409): A growth hormone regimen (EO:0007165) which involves the....
fungal elicitor (EO:0007402): A chemical treatment (EO:0007189) which involves the....
- cerebroside elicitor (EO:0007410): A fungal elicitor treatment (EO:0007402) which.....

Other Classes

mechanical damage (EO:0007373): A physical treatment (EO:0007316) that involves.....
Pseudomonas fluorescens (EO:0007411): A Pseudomonas plant treatment (EO:0007144) involving the exposure to the bacteria Pseudomonas fluorescens.
unknown environment (EO:0007403):

children of plant growth environment (EO:0001002)

drought environment (EO:0007404): A water environment (EO:0007198)...
Hoagland solution (EO:0007405): A hydroponic plant culture media (EO:0007067)..

children of soil environment (EO:0007049) >> soil type (EO:0007155)

clay soil (EO:0007156):
loam soil (EO:0007157):
sandy soil EO:0007158
sandy loam soil EO:0007159

children of soil environment (EO:0007049) >> soil texture (EO:0007050)

loam content (EO:0007004):
sand content (EO:0007051):
organic matter content (EO:0007052):
silt content (EO:0007053):
clay content (EO:0007054):

It seems like there is a lot of overlap between these two branches: soil type and soil texture

Children of ecological environment (EO:0007064) >> flood prone region (EO:0007396)

river bank region (EO:0007081):
sea coast region (EO:0007082):
river delta region EO:0007395

Not sure if we really need "flood prone region". These areas could be flood prone or not

children of fertilizer regimen (EO:0007085) >> natural fertilizer regimen (EO:0007087)

bone meal regimen (EO:0007089):
seaweed extract regimen (EO:0007091):
wood ash regimen (EO:0007092):
fish meal regimen (EO:0007093):

These are not necessarily "natural", should find a better name: could be called "organic", but that may cause confusion with the organic chemicals.

child of fertilizer regimen (EO:0007085) >> chemical fertilizer regimen (EO:0007086) >> nitrogen fertilizer regimen (EO:0007102)

nitrate regimen (EO:0007406):

These are children of 'plant nutrient environment' (EO:0007241), but they are more like treatments. This whole branch should probably moved over to be a treatment.

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Latest revision as of 20:59, 8 December 2014

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