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
- TO:0000050 : inflorescence branching
- TO:0000581 : inflorescence color
- TO:0001002 : inflorescence exsertion
- TO:0000682 : inflorescence height
- TO:0000582 : inflorescence number
- TO:0011002 : inflorescence primary branch attitude
- TO:0000268 : inflorescence shape
- TO:0006031 : inflorescence size
- TO:0000267 : inflorescence type
- TO:0000787 : inflorescence waxiness
- TO:0000623 : involucre bristle length
- TO:0000545 : panicle base to lowest branch
- TO:0020001 : panicle compactness and shape
- TO:0000406 : panicle threshability
- TO:0000641 : primary branch length
- TO:0000657 : spikelet anatomy and morphology trait
- 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
- 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
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.
