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
Grin Global project - Peter Bretting, David Okomuri
Trait lists on Google docs
Triticeae Toolbox Traits for Wheat
Ontology Issues to be worked on:
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...
plant organ anatomy and morphology trait (TO:0000736) and subclasses:
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
- TO:0002751 : inflorescence branch arrangement
- 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.
