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)
We may eventually want to introduce a collective plant system anatomy and morphology trait (TO:xxxxxxx) as a parent term.
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: revised: primary shoot (PO:0006341) (CPS > shoot system) is now a primary shoot system vs stem (PO:0009047) (plant organ > plant axis > shoot axis).
Subclasses:
New sub-class: reproductive shoot system anatomy and morphology trait (TO:0000786): A shoot system anatomy and morphology trait (TO:0000077) that is associated with an reproductive shoot system (PO:0025082).
- inflorescence anatomy and morphology trait (TO:0000373): (CPS > shoot system > reproductive shoot system > inflorescence)
current def'n: Traits associated with changes in the anatomy or structure of the inflorescence and its parts.
new def'n: inflorescence anatomy and morphology trait: A reproductive shoot system anatomy and morphology trait (TO:0000786) that is associated with an inflorescence (PO:0009049).
New sub-class: tassel inflorescence anatomy and morphology trait (TO:0000788):An inflorescence anatomy and morphology trait (TO:0000373) that is associated with an inflorescence (PO:0020126).
- 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
Proposed new new subclasses + definitions:
- bud anatomy and morphology trait: A shoot system anatomy and morphology trait (TO:0000077) which is associated with a bud (PO:0000055).
- axillary bud anatomy and morphology trait: A bud anatomy and morphology trait (TO:id) which is associated with an axillary bud (PO:0004709).
- axillary bud size: An axillary bud anatomy and morphology trait (TO:id) which is associated with the size of an axillary bud (PO:0004709). Refer to size (PATO:0000117)
- axillary bud number: An axillary bud anatomy and morphology trait (TO:id) which is associated with the number of axillary buds (PO:0004709) on a stalk or stem. Refer to number (PATO:0001056)
- axillary bud shape: An axillary bud anatomy and morphology trait (TO:id) which is associated with the shape of an axillary bud (PO:0004709). Refer to shape (PATO:0000052)
- axillary bud prominence: An axillary bud anatomy and morphology trait (TO:id) which is associated with the prominence of an axillary bud (PO:0004709). Refer to prominent (PATO:0014820)
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:
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.
