Plant Trait Ontology

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)

current def'n: This category belongs to traits associated with changes in the anatomy or structure of the plant at organ, tissue or cellular level.

proposed def'n: A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0000003) or one or more constituent cellular components (GO:0005575) contained therein.

comment: Includes traits of plant structures such as plant cell (PO:0009002), portion of plant tissue (PO:0009007), vascular system (PO:0000034)

• new child term and def'n: plant organ trait (TO:XXXXXXX): An anatomy and morphology trait (TO:0000017) which is associated with the anatomy or structure of a plant organ (PO:0009008).
• new term and def'n: plant axis trait (TO:XXXXXXX): plant organ trait (TO:XXXXXXX) which is associated the anatomy or structure of a plant axis (PO:0025004).
• new child term and def'n: shoot axis trait (TO:XXXXXXX): A plant axis trait (TO:XXXXXXX) which is associated with the anatomy or structure of a shoot axis (PO:0025029).
• new term and def'n: branch trait (TO:XXXXXXX): A shoot axis trait (TO:XXXXXXX) which is associated with the anatomy or structure of a branch (PO:0025073).
• new term and def'n: tuber trait (TO:XXXXXXX): A branch trait (TO:XXXXXXX) which is associated with the anatomy or structure of a tuber (PO:0004543).
• new term and def'n: subterranean tuber trait (TO:XXXXXXX): A tuber trait (TO:XXXXXXX) which is associated with the anatomy or structure of a subterranean tuber (PO:0004547).

tuber traitsTerms requested by Syngenta:

tuber (PO:0004543): An enlarged storage branch

subterranean tuber (PO:0004547): A tuber that is below ground

tuber epidermis (PO:0025048): subterranean tuber epidermis

tuber flesh (PO:0025038): subterranean tuber storage parenchyma

tuber eye (PO:0025042): subterranean tuber axillary vegetative bud

requested terms and suggested def'ns:

tuber shape- The shape of the tuber

tuber size- The physical size of the tuber

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)

tuber mass- The mass of the tuber

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

• tuber shape

Proposed new term and def'n: subterranean tuber shape (TO:XXXXXXX): A subterranean tuber trait (TO:XXXXXXX) which is associated with the shape of a subterranean tuber (PO:0004547).

broad synonym: tuber shape

refer to PATO shape: PATO:0000052

• tuber size

Proposed new term and def'n: subterranean tuber size (TO:XXXXXXX): A subterranean tuber trait (TO:XXXXXXX) which is associated with the size of a subterranean tuber (PO:0004547).

refer to PATO size: PATO:0000117

broad synonym: tuber size

• tuber appearance

Proposed new term and def'n: subterranean tuber appearance (TO:XXXXXXX): A subterranean tuber trait (TO:XXXXXXX) which is associated with the appearance of a subterranean tuber (PO:0004547).

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)

broad synonym: tuber appearance

No PATO reference for refer to appearance

• tuber mass

Proposed new term and def'n: subterranean tuber mass (TO:XXXXXXX): A subterranean tuber trait (TO:XXXXXXX) which is associated with the mass of a subterranean tuber (PO:0004547).

broad synonym: tuber mass

refer to PATO mass: PATO:0000125

shoot anatomy and morphology trait:

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

One of the problems with this currently is that it does not include whole plant traits, but has children such as plant height (is_a shoot anatomy and morphology trait)

current is child classes:

• coleoptile color
• coleoptile length
• flower anatomy and morphology trait
• hypocotyl length
• inflorescence anatomy and morphology trait
• leaf anatomy and morphology trait
• mesocotyl length
• plant color
• plant height
• relative shoot elongation under submergence
• shoot habit
• shootless
• stem anatomy and morphology trait
• tiller angle

Child classes of plant structure in PO:

collective plant structure

is_a shoot system [is_a relationship] anther

[is_a relationship] anther theca

[is_a relationship] ceonosorus

[is_a relationship] collective phyllome structure

[is_a relationship] fruit

[is_a relationship] root system

[is_a relationship] shoot system

[is_a relationship] sorus

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)

Other children of plant structure (PO:0009011)

• plant organ
  • coleoptile
  • coleorhiza
  • floral organ
  • phyllome
  • plant axis
  • plant gametangium
  • sporangium
  • sporophyte foot

• portion of plant tissue (PO:0009007)

• cardinal organ part

• plant cell (PO:0009002)

• vascular system (PO:0000034)

• collective organ part structure

• embryo plant structure (PO:0025099)

• in vitro plant structure

• ovary
• rhizoid
• seed
• trichome
• whole plant

whole plant trait TO:0000398

has been obsoleted, maybe we should consider bringing back?