Difference between revisions of "Plant Trait Ontology"

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[[anatomy and morphology related trait (TO:0000017)]]
 
[[anatomy and morphology related trait (TO:0000017)]]
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==[https://sourceforge.net/tracker/?func=detail&aid=3487511&group_id=76834&atid=835557 tuber traits]==
 
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Terms requested by Syngenta (in bold):
 
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'''tuber''' (PO:0004543): An enlarged storage branch (PO:0025073)
 
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probably should be: subterranean tuber (PO:0004547): A tuber (PO:0004543) that is below ground
 
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'''tuber epidermis''' (PO:0025046): A portion of shoot axis epidermis that is part of a tuber (PO:0004543).
 
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probably should be: subterranean tuber epidermis (PO:0025048): A tuber epidermis (PO:0025046) that is part of a subterranean tuber (PO:0004547).
 
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tuber axillary vegetative bud (PO:0025040): An axillary vegetative bud (PO:0004712) that is part of a tuber (PO:0004543).  related synonym: '''tuber eye'''
 
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probably should be: subterranean tuber axillary vegetative bud (PO:0025042): A tuber axillary vegetative bud (PO:0025040) that is part of a subterranean tuber (PO:0004547).
 
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broad synonym:'''tuber eye'''
 
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tuber storage parenchyma (PO:0025036): A portion of storage parenchyma (PO:0025035) that is part of a tuber (PO:0004543). exact synonym:'''tuber flesh'''
 
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probably should be: subterranean tuber storage parenchyma (PO:0025038): A portion of tuber storage parenchyma (PO:0025036) that is part of a subterranean tuber (PO:0004547).
 
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Narrow Synonym: '''potato tuber''' flesh
 
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===requested terms and suggested def'ns:===
 
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tuber shape- The shape of the tuber
 
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tuber size- The physical size of the tuber
 
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tuber appearance- The overall appearance of the tuber. A 1-9 scale is used, with 1 the lowest score (very poor) and 9 the highest (excellent)
 
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tuber mass- The mass of the tuber
 
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[[File:Tuber.png]]
 
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In the PO: A '''tuber''' is a '''branch''' which is a '''shoot axis''';  shoot axis is_a '''plant_axis''';  which is_a '''plant organ''' part_of the '''shoot system'''
 
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* '''tuber shape'''
 
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Proposed new term and def'n:
 
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'''subterranean tuber shape''' (TO:0000743): A subterranean tuber trait (TO:0000742) which is associated with the shape of a subterranean tuber (PO:0004547).
 
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broad synonym: tuber shape
 
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refer to PATO shape: PATO:0000052
 
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* '''tuber size'''
 
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Proposed new term and def'n: '''subterranean tuber size''' (TO:0000744): A subterranean tuber trait (TO:0000742) which is associated with the size of a subterranean tuber (PO:0004547).
 
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refer to PATO size: PATO:0000117
 
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broad synonym: tuber size
 
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* '''tuber appearance'''
 
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Proposed new term and def'n: '''subterranean tuber appearance''' (TO:0000745): A subterranean tuber trait (TO:0000742) which is associated with the appearance of a subterranean tuber (PO:0004547).
 
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comment: A 1-9 scale is used to score the overall appearance of the tuber, with 1 the lowest score (very poor) and 9 the highest (excellent)
 
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broad synonym: tuber appearance
 
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No PATO reference for refer to appearance
 
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* '''tuber mass'''
 
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Proposed new term and def'n: '''subterranean tuber mass''' (TO:0000746): A subterranean tuber trait (TO:0000742) which is associated with the mass of a subterranean tuber (PO:0004547).
 
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broad synonym: tuber mass
 
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refer to PATO mass: PATO:0000125
 
  
 
==shoot anatomy and morphology trait (TO:0000077)==
 
==shoot anatomy and morphology trait (TO:0000077)==

Revision as of 05:16, 20 April 2012

This page will be a place to keep track of the work on developing the Plant Trait Ontology


New:

Call for papers: Knowledge Engineering and Ontology Development

Crop Plant Trait Ontology paper

Also: Ontologies and semantic technologies for agricultural knowledge in practice

Related Wiki Pages and Links:

Details about the plans for the Crop_Ontology_Workshop_at_OSU,_2012

Work on the wood traits: Goal_3._Wood_qualities_and_phenotypes

TO Tracker on SourceForge

Trait Ontology on Bioportal: TO

Links to Collaborator Sites:

GCP Phenotype and Trait Ontology

Triticeae Toolbox

Triticeae Toolbox Barley

Trait Descriptions


Trait lists on Google docs

Wood Traits

Crop Traits List

Triticeae Toolbox Traits for Wheat

Bioenergy Traits

Ontology Issues:

root term: plant trait (TO:0000387)

need to fix definition of plant trait to include cellular components and biochemical traits etc

current def'n: A measurable or observable characteristic of a plant anatomical entity (PO:0000003) and/or a plant structure development stage (PO:0009012).

new proposed def'n: A measurable or observable characteristic of a cellular component (GO:0005575), biological process (GO:0008150) or molecular function (GO:0003674) that is part of, or has participant a plant anatomical entity (PO:0000003)and or a plant structure development stage (PO:0009012).

Comment: This includes physiological, molecular and biochemical traits as well.

background on the GO classes:

  • cellular component (GO:0005575): The part of a cell or its extracellular environment in which a gene product is located.

Includes cells and parts of cells like membranes, organelles, symplast, apoplast, plant extracellular matrix (The matrix external to the plant plasma membrane, composed of the cell wall and middle lamella), parts of the pollen wall (exine (including sexine), intine), pollen coat,

  • biological process (GO:0008150): Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

Includes: Processes important to plants such as: growth, development, reproduction, senescence, respiration, photosynthesis, metabolism, signaling, response to abiotic (e.g. cold acclimation, vernalization, heat, flooding, drought, response to herbicide, wounding, inorganic substance) and biotic stress (responses to bacteria, fungi, herbivores, insects, viruses, symbionts, defense response, detection of stress, incompatible and compatible responses), rhythmic process (e.g. circadian rhythm > circadian regulation of gene expression), seed development and germination, phloem transport, etc etc..... nitrogen fixation .

  • molecular function (GO:0003674): Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level.

Includes all the enzyme activities such as catalysis of a biochemical reaction, regulation, binding, nucleic acid binding (transcription factor), receptor activity, transporter activity,etc

anatomy and morphology related trait (TO:0000017)

shoot anatomy and morphology trait (TO:0000077)

current def'n: Traits associated with changes in the anatomy or structure of the shoot and its parts.

One of the many problems with this currently is that it does not include whole plant traits, but has children such as plant height.

propose new name and def'n:

shoot system trait (TO:0000077): An anatomy and morphology trait (TO:0000017) which is associated with the anatomy or morphology of a shoot system (PO:0009006).

current is child classes (with PO class):

  • flower anatomy and morphology trait (CPS > shoot system > reproductive shoot system > flower)
  • inflorescence anatomy and morphology trait (CPS > shoot system > reproductive shoot system > inflorescence)

These could stay in this renamed class; shoot system trait (TO:0000077)


  • coleoptile color (plant organ)
  • coleoptile length (plant organ)
  • leaf anatomy and morphology trait (plant organ> phyllome> leaf)

all of this group should go under the new class: plant organ trait (TO:0000736), above


  • relative shoot elongation under submergence (plant organ > plant axis > shoot axis (syn: shoot))
  • shootless (plant organ > plant axis > shoot axis (syn: shoot))
  • shoot habit (plant organ > plant axis > shoot axis (syn: shoot))
  • stem anatomy and morphology trait (plant organ > plant axis > shoot axis > stem)
  • tiller angle (plant organ > plant axis > shoot axis >shoot-borne shoot system> axillary shoot system >basal axillary shoot (syn: tiller))

all of this group should go under the new class: shoot axis trait (TO:0000739), above


  • hypocotyl length (COP > shoot internode > stem internode > hypocotyl)
  • mesocotyl length (COP > shoot internode > stem internode > mesocotyl)
  • plant color (whole plant)
  • plant height (whole plant)

Not sure where to put these right now- TBA

Other shoot anatomy and morphology trait

plant cell anatomy and morphology trait

    • plant cell length
    • plant cell shape
    • plant cell size

cell organelle structure trait

    • plastid development trait

fruit structure trait

    • fruit abscission zone size
    • fruit shape
    • fruit size

seed anatomy and morphology trait

    • embryo related trait
    • endosperm related trait
    • seed coat color
    • seed color
    • seed shape
    • seed texture

Also:

  • root anatomy and morphology trait
  • vascular tissue related trait
  • plant aspect (should go under whole plant)


whole plant trait TO:0000398

has been obsoleted, maybe we should consider bringing back?

requested terms:

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