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:
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:
User requested terms:
From: Syngenta (see Crop Traits Google doc)
Cotyledon traits:
PO term: cotyledon (PO:0020030): A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
hierarchy: plant organ > phyllome >leaf > vascular leaf > cotyledon
make children of new class: plant organ anatomy and morphology trait (TO:0000736): An anatomy and morphology trait (TO:0000017) which is associated with a plant organ (PO:0009008).
Add new classes:
- phyllome anatomy and morphology trait (TO:xxxxxxx): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a phyllome (POID).
- existing class: leaf anatomy and morphology trait (TO:0000419): Traits associated with changes in the anatomy or structure of the leaf and its parts.
this refers only to vascular leaves, there are 625 annotations on Gramene for this class
propose we rename to vascular leaf anatomy and morphology trait (TO:0000419). this will make it clear that it is specific to vascular leaves. See revised def'n below. This will allow all the existing children to stay on the vlamt and won't mess up the annotations as TO# will stay the same.
- new term: leaf anatomy and morphology trait (TO:xxxxxxx): A phyllome anatomy and morphology trait (TO:xxxxxxx) which is associated with a leaf (POID).
- vascular leaf anatomy and morphology trait (TO:0000419): revised def'n: A leaf anatomy and morphology trait (TO:xxxxxxx) which is associated with a vascular leaf (POID).
- cotyledon anatomy and morphology trait (TO:xxxxxxx): A vascular leaf anatomy and morphology trait (TO:0000419) which is associated with a cotyledon (POID).
Requested terms:
- cotyledon color(TO:xxxxxxx): A cotyledon anatomy and morphology trait (TO:xxxxxxx) which ..... a cotyledon(POID).
- cotyledon number (TO:xxxxxxx): A cotyledon anatomy and morphology trait (TO:xxxxxxx)
- cotyledon size (TO:xxxxxxx): A cotyledon anatomy and morphology trait (TO:xxxxxxx) which
hypocotyl and mescotyl
this section is in progress....
- hypocotyl color
Existing TO terms: these are currently children of shoot system anatomy and morphology trait
- hypocotyl length (COP > shoot internode > stem internode > hypocotyl)
- mesocotyl length (COP > shoot internode > stem internode > mesocotyl)
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.
shoot system anatomy and morphology trait (TO:0000077)
current (now former) name and def'n: shoot anatomy and morphology trait (TO:0000077): 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.
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.
Reassigning the child classes
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 anatomy and morphology trait (TO:0000077)
- 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
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?
Can we just use "anatomy trait"? It would make all these names less cumbersome.
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?
