Plant Trait Ontology

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

Go here for more info on Changes to the TO- Spring 2012

For more concise notes: Summary New TO Terms- Spring 2012

New:

Link to AMIGO TO Browser....under development!

Upcoming Presentations and Publications

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:

Link to TO on Gramene

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

Go here for more info on Changes to the TO- Spring 2012

Links to Collaborator Sites:

GCP Phenotype and Trait Ontology

Sol Genomics Network

SoyBase

Triticeae Toolbox

Triticeae Toolbox Barley

Trait Descriptions

Grin Global project - Peter Bretting, David Okomuri

Trait lists on Google docs

Wood Traits

Crop Traits List

Triticeae Toolbox Traits for Wheat

Bioenergy Traits

Duplicated terms:

• stem senescence (TO:0001036) def: "A measurement of aging of stem."

is_a: TO:0000361 ! stem anatomy and morphology trait

and

• stem senescence (TO:0020085) def: "A trait to measure the stem senescence."

is_a: TO:0000654 ! shoot development trait

Same problem as before:

• total water soluble content (TO:0002711): def: "The concentration of water soluble components in the plant as determined by refractive index."

is_a: TO:0000281 ! metabolite content related trait

and

• total water soluble content (TO:0020088): def: "A trait to measure the concentration of water soluble components in the plant as determined by refractive index."

comment: This trait is usually highly correlated with total soluble sugar content (TO:0000340). Often determined in fresh tissue. synonym: "total dissolved solids content" EXACT [] is_a: TO:0000281 ! metabolite content related trait

• check definition of: TO:0020085

the term name itself should never be used (except some particular cases) to define a concept...

cardinal organ part anatomy and morphology traits (TO:0000754)

New class to organize this important group of plant structures, which includes about 50 direct is_a children such as the parts of the leaf, plant axis, root, shoot axis, sporangium, archegonium, ovary, palea, petiole, etc etc

Also includes:

• parts of seed (PO:0009010) (is_a plant structure): hilum (PO:0020063), hilum groove (PO:0004719); arilloid (PO:0019022); seed funicle (PO:0006332)(>stalk > COP); seed raphe (PO:0006331)

• parts of the fruit (is_a collective plant structure): ,

COP also includes the shoot internode and all its child classes: PO:0025080 : branch internode PO:0006326 : inflorescence internode PO:0025204 : rhizome internode PO:0020142 : stem internode

Add new terms:

• cardinal organ part anatomy and morphology trait (TO:0000754): An anatomy and morphology trait (TO:0000017) which is associated with a cardinal organ part (PO:0025001).

completed

plant organ anatomy and morphology trait (TO:0000736) and subclasses:

shoot axis anatomy and morphology trait (TO:0000739)

• inflorescence axis anatomy and morphology trait (TO:0000782): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with an inflorescence axis (PO:0020122).

• • inflorescence branch anatomy and morphology trait (TO:xxxxxxx): A inflorescence axis anatomy and morphology trait (TO:0000782) which is associated with an inflorescence branch (PO:ID).

• • • tassel branch anatomy and morphology trait (TO:xxxxxxx): An inflorescence branch anatomy and morphology trait (TO:xxxxxxx) which is associated with a tassel branch (PO:ID)

User requests:

• tassel type: Branching type of tassel whether primary or primary-secondary or primary-secondary- tertiary
• Tassel branches dry weight: The dry weight of tassel branches (grams) just prior to pollen shed.

• Tassel branches number: Number of branches of tassel

Other existing shoot axis classes:

• stem anatomy and morphology trait (plant organ > plant axis > shoot axis > stem)

• 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))

• tiller angle (plant organ > plant axis > shoot axis >shoot-borne shoot system> axillary shoot system >basal axillary shoot (syn: tiller))

user requested: peduncle traits

plant structure > plant organ > plant_axis >shoot axis > peduncle

peduncle (PO:0009053): A shoot axis that extends from the last foliage leaf on a stem or branch until the next distal node.

Comment: In plants with single flowers, the peduncle ends with a flower. In plants with inflorescences, the peduncle is the basal end of the primary inflorescence axis, and it ends where the inflorescence begins to branch. The peduncle marks the axial transition from vegetative to reproductive growth. In branching inflorescences, the second order inflorescence axis from the point at which it leaves the main axis up to the point at which it branches again may be called the second order peduncle. Higher order peduncles are also possible.

parent: shoot axis anatomy and morphology trait (TO:0000739): A plant axis trait (TO:0000738) which is associated with a shoot axis (PO:0025029).

New term: peduncle anatomy and morphology trait (TO:0000776): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with a peduncle (PO:0009053).

peduncle waxiness: A peduncle anatomy and morphology trait (TO:0000776) which is associated with a visual observation of the presence of cuticular wax (PO:0025386).

No PATO term for waxiness- suggested new term on SF. suggested definitions: the state or quality of being waxy or the presence of long chain aliphatic lipids on the surface of an organism.

see related PO terms:

• cuticular wax (PO:0025386)-A portion of plant substance comprised predominantly of very long chain aliphatic lipids and is part of a plant cuticle.

comment: Also includes triterpenoids and minor secondary metabolites, such as sterols and flavonoids. May be embedded within or external to the layer of cutin of the cuticle proper. Phenotypically, wax is distinguished as the glaucous or whitish bloom on a part of a plant shoot system that corresponds to crystalloid epicuticular wax with light scattering capacity.

• • intercuticular wax (PO:0025389)- A portion of cuticular wax that is an amorphous mixture of lipids embedded in the cutin of a cuticle proper.

comment: The intercuticular wax is located adjacent to the cell wall.

• • epicuticular wax(PO:0025388)- A portion of cuticular wax that forms crystalloids or a smooth film on the exterior of a cuticle.

comment:Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.

Moved existing terms to new parent and redefined:

• peduncle length (TO:0002691): A peduncle anatomy and morphology trait (TO:0000776) which is associated with the length of a peduncle (PO:0009053). Refer to length (PATO:0000122)
• peduncle width (TO:0000649): A peduncle anatomy and morphology trait (TO:0000776) which is associated with the width of a peduncle (PO:0025386). Refer to width (PATO:0000921)
• peduncle top diameter (TO:0000546): A peduncle anatomy and morphology trait (TO:0000776) which is associated with the diameter at the tip of the peduncle (PO:0009053). Refer to diameter (PATO:0001334)

completed

see also: TO:0000545 : panicle base to lowest branch: "peduncle length from panicle base to first primary branch" [related synonym]

shoot system anatomy and morphology trait (TO:0000077)

We may eventually want to introduce a collective plant system anatomy and morphology trait (TO:xxxxxxx) as a parent term.

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

The PO class shoot system (PO:0009006) includes several important subclasses such as: bud, primary shoot, reproductive shoot system (inflorescence, flower, spikelet, infructescence, reproductive bud, etc) and others.

PO note: look at primary shoot (PO:0006341) (CPS > shoot system) vs stem (PO:0009047) (plant organ > plant axis > shoot axis). How can primary shoot be a shoot system?? -needs to be resolved.

Subclasses:

Need new sub-class: reproductive shoot system anatomy and morphology trait (TO:xxxxxxx): A shoot system anatomy and morphology trait (TO:0000077) that is associated with an reproductive shoot system (PO:0025082).

*inflorescence anatomy and morphology trait (TO:0000373): (CPS > shoot system > reproductive shoot system > inflorescence)

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

new def'n: inflorescence anatomy and morphology trait: A reproductive shoot system anatomy and morphology trait (TO:xxxxxxx) that is associated with an inflorescence (PO:0009049).

Need new sub-class: tassel inflorescence anatomy and morphology trait (TO:xxxxxxx):An inflorescence anatomy and morphology trait (TO:0000373) that is associated with an inflorescence (PO:0020126).

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

New def'n: A reproductive shoot system anatomy and morphology trait (TO:xxxxxxx) that is associated with an flower (PO:xxxxxxx).

User requested:

• flower shape

other

• plant color (TO:0000708): - move to 'stature and vigor trait'

Current def'n: The color of the plant.

new def'n: A stature and vigor trait (TO:0000133) which is associated with the color of a plant. Refer to color PATO:0000014.

• plant height (TO:0000207): has two is_a parents: 'shoot system anatomy and morphology trait' ; 'stature and vigor trait'

- this should just be a "stature and vigor trait, rather than keeping it in the Anatomy and Morphology hierarchy as well..

Current def'n: Actual measurement of plant height from soil surface to the highest point in plant as identified in the study.

new def'n: A stature and vigor trait (To:0000133) which is associated with the height of a plant. Refer to height PATO:0000119.

completed

fruit structure trait (TO:0000357)

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

fruit (PO:0009001) is_a collective plant structure, along with anther, root system and shoot system, sorus and cenosorus.

Should we have a mid-level class to organize these?

Proposed hierarchy:

anatomy and morphology trait (TO:0000017)

>collective plant structure anatomy and morphology trait (proposed)

>>fruit anatomy and morphology trait (TO:0000357)

>>shoot system anatomy and morphology trait (TO:0000077)

>>root system anatomy and morphology trait (proposed)

>>anther anatomy and morphology trait (proposed)

Could add additional children as needed later.

• fruit abscission zone size
• fruit shape
• fruit size

Other anatomy and morphology trait classes:

plant cell anatomy and morphology trait (TO:0002683)

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

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

cell organelle structure trait (TO:0002713)

Need to resolve whether this is an anatomy and morphology related trait (TO:0000017) or a growth and development trait (TO:0000357).

current def'n: Trait(s) associated with phenotypes observed for abnormal development of organelle structure and biogenesis.

• plastid development trait

seed anatomy and morphology trait (TO:0000184)

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

seed (PO:0009010):A plant structure that develops from an ovule and has as parts an embryo enclosed in a seed coat. [source: POC:curators]

comment: A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms).

need to fix this comment- the reproductive unit of the grasses is a caryopsis, which is_a fruit.

• embryo related trait (is_a whole plant)
• endosperm related trait
• seed coat color
• seed color
• seed shape
• seed texture

new term plant aspect (TO:0000737)

Should this go under stature or vigor trait (TO:0000133)? - refers to a whole plant

whole plant trait TO:0000398

has been obsoleted, maybe we should consider bringing back?

Other top level classes:

growth and development trait

growth and development trait (TO:0000357): Traits associated with observing effects on the development of the plant or plant parts.