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:

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

stem internode traits:

PO hierarchy: cardinal organ part > shoot internode > stem internode > hypocotyl (PO:0020100), mesocotyl (PO:0020037) and epicotyl (PO:0020035)

• shoot internode anatomy and morphology trait (TO:0000755): A cardinal organ part anatomy and morphology trait (TO:0000754) which is associated with a shoot internode (PO:0005005).

• stem internode anatomy and morphology trait (TO:0000756): A shoot internode anatomy and morphology trait (TO:0000755) which is associated with a stem internode (PO:0020142).

• hypocotyl anatomy and morphology trait (TO:0000757): A stem internode anatomy and morphology trait (TO:0000756) which is associated with a hypocotyl (PO:0020100).

• mesocotyl anatomy and morphology trait (TO:0000758): A stem internode anatomy and morphology trait (TO:0000756) which is associated with a mesocotyl (PO:0020037).

Existing TO terms: these are currently children of shoot system anatomy and morphology trait

• hypocotyl length (TO:0006065): A hypocotyl anatomy and morphology trait (TO:0000757) which is associated with the length of a hypocotyl (PO:0020100). Refer to length PATO:0000122

• mesocotyl length (TO:0000544): A mesocotyl anatomy and morphology trait (TO:0000758) which is associated with the length of a mesocotyl (PO:0020037). Refer to length PATO:0000122

completed

user requested: hypocotyl color

From: Syngenta (see Crop Traits Google doc)

• hypocotyl color (TO:0000759): A hypocotyl anatomy and morphology trait (TO:0000757) which is associated with the color of a hypocotyl (PO:0020100). Refer to color PATO:0000014

add comment: color of hypocotyl at or shortly after emergence (use PO stage term).

Need to create terms to capture the values: see google docs:

these may need to be reworded slightly- look at other examples in the TO

color of hypocotyl at or shortly after emergence: - green, green with bronze band, purple, dark purple. PATO terms for: green, green with bronze band, purple, dark purple.

• hypocotyl green (TO:xxxxxxx): A hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color green (PATO:0000320).

Refer to: color (PATO:0000014); green (PATO:0000320)

• hypocotyl green with bronze band (TO:xxxxxxx): A hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color green (PATO:0000320) with a bronze (PATO: TBA) band.

• hypocotyl purple (TO:xxxxxxx): A hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color purple (PATO:0000951).

Refer to: color (PATO:0000014); purple: PATO:0000951

• hypocotyl dark purple (TO:xxxxxxx): A hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color dark purple (PATO:0001259).

Refer to: color (PATO:0000014); dark purple: PATO:0001259

We will need to request a term for bronze from PATO

user requested: petiole traits

From: Syngenta (see Crop Traits Google doc)

cardinal organ part > stalk > petiole

petiole (PO:0020038): A stalk of a leaf.

Add new terms:

stalk anatomy and morphology trait (TO:xxxxxxx): A cardinal organ part anatomy and morphology trait (TO:0000754) which is associated with a stalk (PO:id).

petiole anatomy and morphology trait (TO:xxxxxxx): A stalk anatomy and morphology trait (TO:xxxxxxx): which is associated with a petiole (PO:id).

Add new terms:

petiole length (TO:xxxxxxx): A petiole anatomy and morphology trait (TO:xxxxxxx)that is associated with the length (PATO:id) of a petiole (PO:0020038).

petiole shape(TO:xxxxxxx): A petiole anatomy and morphology trait (TO:xxxxxxx) that is associated with the shape (PATO:id) of a petiole (PO:0020038).

petiole size (TO:xxxxxxx): A petiole anatomy and morphology trait (TO:xxxxxxx) that is associated with the size (PATO:id) of a petiole (PO:0020038).

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-
• intercuticular wax
• epicuticular wax

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

• plant color (whole plant)
• plant height (whole plant)

Not sure where to put these right now- TBA

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.