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

plant organ anatomy and morphology traits (TO:0000736)

• phyllome anatomy and morphology trait (TO:0000747)

PO hierarchy: plant organ > phyllome >leaf > vascular leaf > cotyledon

make children of new class: plant organ anatomy and morphology trait (TO:0000736): An anatomy and morphology trait (TO:0000017) which is associated with a plant organ (PO:0009008).

Add new classes:

• phyllome anatomy and morphology trait (TO:0000747): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a phyllome (PO:0006001).

• existing class: leaf anatomy and morphology trait (TO:0000419): Traits associated with changes in the anatomy or structure of the leaf and its parts.

this refers only to vascular leaves, there are 625 annotations on Gramene for this class

propose we rename to vascular leaf anatomy and morphology trait (TO:0000419). this will make it clear that it is specific to vascular leaves. See revised def'n below. This will allow all the existing children to stay on the vlamt and won't mess up the annotations as TO# will stay the same.

• new term: leaf anatomy and morphology trait (TO:0000748): A phyllome anatomy and morphology trait (TO:0000747) which is associated with a leaf (PO:0025034).

• vascular leaf anatomy and morphology trait (TO:0000419): revised def'n: A leaf anatomy and morphology trait (TO:0000748) which is associated with a vascular leaf (PO:0009025).

• cotyledon anatomy and morphology trait (TO:0000749): A vascular leaf anatomy and morphology trait (TO:0000419) which is associated with a cotyledon (PO:0020030).

Requested cotyledon trait terms:

From: Syngenta (see Crop Traits Google doc)

PO term: cotyledon (PO:0020030): A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003).

• cotyledon color(TO:0000750): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the shape of a cotyledon(PO:0020030).

refer to PATO shape: PATO:0000052

• cotyledon number (TO:0000751): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the number of cotyledons (PO:0020030).

refer to PATO count: PATO:0000070

• cotyledon size (TO:0000752): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the size of a cotyledon(PO:0020030).

refer to PATO size: PATO:0000117

coleoptile trait terms

PO hierarchy: plant organ > coleoptile >embryo coleoptile (PO:00252860 and seedling coleoptile (PO:0025287)

Existing TO terms:

• coleoptile color (TO:0000244) def: "Measure of color of the coleoptile in the germinating seedling." [GR:pj]

synonym: "COLCL" RELATED

is_a: TO:0000064 ! embryo related trait

is_a: TO:0000736 ! plant organ anatomy and morphology trait

• coleoptile length (TO:0001007) def: "Measurement of the length of the coleoptile in the germinating seed." [GR:pj]

is_a: TO:0000736 ! plant organ anatomy and morphology trait

Need new class: coleoptile anatomy and morphology trait (TO:0001007): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).

Cardinal organ part anatomy and morphology traits (TO:xxxxxx)

this section is in progress....

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, seed (hilum (PO:0020063), hilum groove (PO:0004719)????), archegonium, fruit, ovary, palea, petiole, etc etc

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

• shoot internode anatomy and morphology trait (TO:xxxxxx): fill in def'n

• stem internode anatomy and morphology trait (TO:xxxxxx): fill in def'n

• hypocotyl anatomy and morphology trait (TO:xxxxxx): fill in def'n

stem internode traits

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

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

• hypocotyl length (COP > shoot internode > stem internode > hypocotyl)
• mesocotyl length (COP > shoot internode > stem internode > mesocotyl)

===user

• hypocotyl color

root anatomy and morphology trait (TO:0000043)

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

propose revised def'n: root anatomy and morphology trait (TO:0000043): A plant axis anatomy and morphology trait (TO:0000738) that is associated with the root (PO:0025025).

make a child of the new class: plant axis anatomy and morphology trait (TO:0000738)

root (PO:0025025): A plant axis that is part of a root system. [source: POC:curators]

PO Comment: Commonly thought of as one of the three basic parts of the seed plant body. A plant stucture (organ) that is usually underground and does not bear leaves and only rarely shoots, is usually more or less positively geotropic, is endogenous in origin, indeterminate in growth and often with secondary thickening.

PO hierarchy: plant organ > plant axis > shoot axis > root

PO Children of root:

• PO:0020127: primary root
• PO:0020121: lateral root
• PO:0000045: embryo root
• PO:0025002: basal root (broad: adventitious root)
• PO:0000042: shoot-borne root (broad: adventitious root)

note issue with children: adventitious root traits: in the PO adventitious root is a broad synonym of shoot-borne root and also basal root, depending where it arises from.

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)

• 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

Ok

• 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

• 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

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?

Can we just use "anatomy trait"? It would make all these names less cumbersome.

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?