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

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

user requested: peduncle traits (plant organ anatomy and morphology trait)

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.

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

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

peduncle anatomy and morphology trait (TO:xxxxxxx): 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:xxxxxxx) which is associated with a visual observation of the presence of wax (use appropriate PO term)

No PATO term for waxiness.

see related PO terms: look up POids and definitions.

• 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.

Move existing terms to new parent:

• peduncle length TO:0002691
• peduncle width (TO:0000649)
• TO:0000546 : peduncle top diameter [show def] plant trait ontology

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)

current (now former) name and def'n: shoot anatomy and morphology trait (TO:0000077): 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 a hodge podge of children, including terms describing plant organs and cardinal organ parts and whole plant traits such as plant height.

new name and def'n: 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.

Reassigning the child classes

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 anatomy and morphology trait (TO:0000077)

• 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 anatomy and morphology trait (TO:0000739), above

Ok, done

• 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

Duplicated terms:

• [Term] id: TO:0001036

name: stem senescence def: "A measurement of aging of stem." [GR:cwt] synonym: "culm senescence" RELATED [] is_a: TO:0000361 ! stem anatomy and morphology trait

and

• [Term]

id: TO:0020085 name: stem senescence def: "A trait to measure the stem senescence." [GR:pj] synonym: "culm senescence" EXACT [] is_a: TO:0000654 ! shoot development trait created_by: jaiswalp creation_date: 2011-08-19T03:34:31Z

Same problem as before:

• [Term] id: TO:0002711

name: total water soluble content def: "The concentration of water soluble components in the plant as determined by refractive index." [GR:pj] is_a: TO:0000281 ! metabolite content related trait

and

• [Term] id: TO:0020088

name: total water soluble content 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 created_by: jaiswalp creation_date: 2011-08-19T03:47:00Z

• check definition of: TO:0020085

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

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.