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:
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
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:
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.
New term: shoot axis anatomy and morphology trait (TO:0000077)
current def'n: 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.
propose 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.
needs updated on OE
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 trait (TO:0000077)
Ok
- 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
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?
