Difference between revisions of "Plant Trait Ontology"
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===user requested: peduncle traits (plant organ anatomy and morphology trait)=== | ===user requested: peduncle traits (plant organ anatomy and morphology trait)=== | ||
Revision as of 16:37, 11 May 2012
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:
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:
cardinal organ part anatomy and morphology traits (TO:0000754)
New class to organize this important group of plant structures, which includes about 50 direct is_a children such as the parts of the leaf, plant axis, root, shoot axis, sporangium, archegonium, ovary, palea, petiole, etc etc
Also includes:
- parts of seed (PO:0009010) (is_a plant structure): hilum (PO:0020063), hilum groove (PO:0004719); arilloid (PO:0019022); seed funicle (PO:0006332)(>stalk > COP); seed raphe (PO:0006331)
- parts of the fruit (is_a collective plant structure): ,
COP also includes the shoot internode and all its child classes: PO:0025080 : branch internode PO:0006326 : inflorescence internode PO:0025204 : rhizome internode PO:0020142 : stem internode
Add new terms:
- cardinal organ part anatomy and morphology trait (TO:0000754): An anatomy and morphology trait (TO:0000017) which is associated with a cardinal organ part (PO:0025001).
completed
user requested: peduncle traits (plant organ anatomy and morphology trait)
peduncle (PO:0009053): A shoot axis that extends from the last foliage leaf on a stem or branch until the next distal node.
Comment: In plants with single flowers, the peduncle ends with a flower. In plants with inflorescences, the peduncle is the basal end of the primary inflorescence axis, and it ends where the inflorescence begins to branch. The peduncle marks the axial transition from vegetative to reproductive growth. In branching inflorescences, the second order inflorescence axis from the point at which it leaves the main axis up to the point at which it branches again may be called the second order peduncle. Higher order peduncles are also possible.
plant structure > plant organ > plant_axis >shoot axis > peduncle
parent: shoot axis anatomy and morphology trait (TO:0000739): A plant axis trait (TO:0000738) which is associated with a shoot axis (PO:0025029).
peduncle anatomy and morphology trait (TO:xxxxxxx): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with a peduncle (PO:0009053).
peduncle waxiness: A peduncle anatomy and morphology trait (TO:xxxxxxx) which is associated with a visual observation of the presence of wax (use appropriate PO term)
No PATO term for waxiness.
see related PO terms: look up POids and definitions.
- cuticular wax(PO:0025386)-A portion of plant substance comprised predominantly of very long chain aliphatic lipids and is part of a plant cuticle.
comment: Also includes triterpenoids and minor secondary metabolites, such as sterols and flavonoids. May be embedded within or external to the layer of cutin of the cuticle proper. Phenotypically, wax is distinguished as the glaucous or whitish bloom on a part of a plant shoot system that corresponds to crystalloid epicuticular wax with light scattering capacity.
- intercuticular wax(PO:0025389)- A portion of cuticular wax that is an amorphous mixture of lipids embedded in the cutin of a cuticle proper.
comment: The intercuticular wax is located adjacent to the cell wall.
- epicuticular wax(PO:0025388)- A portion of cuticular wax that forms crystalloids or a smooth film on the exterior of a cuticle.
comment:Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.
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)
- 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, done
- 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?
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.
