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...

shoot system anatomy and morphology trait (TO:0000077)

- large number of other children of inflorescence anatomy and morphology trait that need a lot of work:

• TO:0020077 : head drop
• inflorescence branch arrangement (TO:0002751): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the arrangement of inflorescence branches (PO:0009081).
• inflorescence branching (TO:0000050): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the extent of branching usually sets the tone for shape and compactness of the inflorescence (PO:0009049).
• TO:0000641 : primary branch length
• TO:0011002 : inflorescence primary branch attitude
• inflorescence color (TO:0000581): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the color of an inflorescence (PO:0009049).
• inflorescence exsertion (TO:0001002): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the exsertion of an inflorescence (PO:0009049).
• inflorescence height (TO:0000682): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the height of an inflorescence (PO:0009049) measured from ground to the attachment point.
• inflorescence number (TO:0000582): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the average number of inflorescence (PO:0009049) per plant in a study.
• inflorescence shape (TO:0000268): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the shape of an inflorescence (PO:0009049).
• inflorescence size (TO:0006031): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the variation in size of inflorescence (PO:0009049).
• inflorescence type (TO:0000267): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the variation in the type of inflorescence, wither due to extent and number of branching, branch angles or modified form of the inflorescence (PO:0009049).
• inflorescence waxiness (TO:0000787): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the waxiness of an inflorescence (PO:0009049).
• panicle base to lowest branch (TO:0000545): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the length of the region between the panicle base to the lowest (the first) primary panicle branch.
• panicle compactness and shape (TO:0020001): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the compactness and shape of a panicle.
• panicle threshability (TO:0000406): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the percentage of shattered grains, determined by firmly grasping and pulling the hand over the panicle.
• spikelet anatomy and morphology trait (TO:0000657): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with changes in the anatomy or structure of the spikelet (PO:0009051) and its parts.
• TO:0000623 : involucre bristle length

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

New def'n: A reproductive shoot system anatomy and morphology trait (TO:0000786) that is associated with a flower (PO:xxxxxxx).

User requested:

• flower shape

Other anatomy and morphology trait classes:

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

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.