Difference between revisions of "Plant Trait Ontology"
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anatomy and morphology trait | anatomy and morphology trait | ||
* Continue to restructure terms to follow hierarchy of PO | * Continue to restructure terms to follow hierarchy of PO | ||
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stress trait | stress trait | ||
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** biotic stress trait | ** biotic stress trait | ||
*** traits under these terms need more structure | *** traits under these terms need more structure | ||
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| + | biochemical trait | ||
| + | * has some upper level terms that are very good, others just need to become children of the terms that already exist | ||
| + | |||
| + | |||
| + | growth and development | ||
| + | * waiting to start the hierarchy until the PO has finished restructuring their growth and development traits | ||
| + | |||
| + | |||
| + | stress trait | ||
| + | * should this really be an upper level term? | ||
| + | * does stress qualify as a trait? | ||
| + | |||
| + | |||
| + | stature and vigor/quality traits | ||
| + | * could these two categories be combine? | ||
| + | |||
| + | |||
| + | fertility and sterility traits | ||
| + | * could we incorporate these to stature and vigor/quality or growth and development? | ||
| + | * There only about 4 traits under this category | ||
| + | |||
| + | |||
| + | other misc traits | ||
| + | * this trait should be obsoleted | ||
=Duplicated terms:= | =Duplicated terms:= | ||
Revision as of 19:34, 3 October 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:
Link to AMIGO TO Browser....under development!
DBx Ref Reminder: use "OBO_SF_TO" not "OBO_SF_ID" for links to SourceForge
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:
Order of Top Priority sections
anatomy and morphology trait
- Continue to restructure terms to follow hierarchy of PO
stress trait
- The two upper level terms here are good
- abiotic stress trait
- biotic stress trait
- traits under these terms need more structure
biochemical trait
- has some upper level terms that are very good, others just need to become children of the terms that already exist
growth and development
- waiting to start the hierarchy until the PO has finished restructuring their growth and development traits
stress trait
- should this really be an upper level term?
- does stress qualify as a trait?
stature and vigor/quality traits
- could these two categories be combine?
fertility and sterility traits
- could we incorporate these to stature and vigor/quality or growth and development?
- There only about 4 traits under this category
other misc traits
- this trait should be obsoleted
Duplicated terms:
stem senescence
- 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
- 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
- inflorescence width (TO:0000637)
- inflorescence width (TO:0000804): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the width of an inflorescence (PO:0009049).
- 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)
- TO:0020077 : head drop
- TO:0000623 : involucre bristle length
- floret anatomy and morphology trait (TO:0000274): A flower anatomy and morphology trait (TO:0000499) which is associated with changes in the anatomy or structure of the grass floret and its parts.
- We have lots of floret terms but no PO floret term to use for these terms. Floret is a synonym for flower.
- 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 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.
