Plant Environment Ontology Wiki

Related Links:

EO on Gramene

EO Trackeron SourceForge

EO Bioportal

Unique Identifiers:

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

OSU-POC - 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)

There are 500 classes in this ontology, 50 of them have no definition.

Terms without definitions:

EO:0007004 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

Ontology Issues to be Worked on in Order of Top Priority:

• We need to figure out the identifier numbers used for the ID manager.

plant environment ontology (EO:0007359):

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

• • We propose a revised name of plant environment and a new definition of: Plant treatments, growing conditions, and/or study types.

• • We propose a new comment: These conditions can apply to a whole plant (PO:0000003), a plant population and/or a cultured plant cell (PO:0000005). 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.

Proposed Revision to Hierarchy

New upper level branches for treatment, natural environment, study types

Plant treatment (EO:0001001)

• abiotic treatment
  • chemical treatment
    • inorganic chemical treatment
      • cadmium treatment
      • salt treatment
      • mineral treatment
        • zinc treatment
        • boron treatment
        • nickel treatment
    • organic chemical treatment
      • antibiotic treatment
      • chemical mutagen treatment
      • ethylene treatment
      • plant hormone treatment
        • salicylic acid treatment
  • physical environmental treatment
    • radiation treatment
    • temperature treatment
    • moisture treatment

Growing Conditions

• ecological environment
• physical environment
• seasonal environment
• growth media
• gaseous environment
• nutrient regimen
  • macronutrient regimen
  • micronutrient regimen

abiotic environment (EO:0007191):

There are two children of this term that seem to mean the same thing as abiotic environment: physical environment and ecological environment.

Terms under ecological environment are mostly different environmental regions (i.e. temperate region, tropical region) can we change the name of the parent term or move these terms under a different existing term?

Terms under physical environment are gravity, wind and mechanical damage. We should find a new place for these terms.

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.