Difference between revisions of "Plant Trait Ontology"
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We have to sort out the mixed up terms concerning grains and seeds. | We have to sort out the mixed up terms concerning grains and seeds. | ||
| − | A grain is a caryopsis- a type of fruit (PO:0009001 | + | A grain is a caryopsis- a type of fruit (PO:0009001), while the seed (PO:0009010) is a separate entity, which may be part of the fruit. |
Please go through the TO and look at each term with seed in the name: | Please go through the TO and look at each term with seed in the name: | ||
Revision as of 22:07, 28 January 2013
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
HTML code for graph editor: Click "edit" to see
Display IDs:
$id$
ID Manger settings: TO:$sequence(7,0000001,0020000)$
Upcoming Presentations and Publications
Call for papers: Knowledge Engineering and Ontology Development
Crop Plant Trait Ontology paper
Related Wiki Pages and Links:
Link to TO on Gramene
Details about 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 Okamura
Trait lists on Google docs
Triticeae Toolbox Traits for Wheat
Ontology Issues to be worked on:
Order of Top Priority sections
For the week of Jan 28th to Feb 1st:
We have to sort out the mixed up terms concerning grains and seeds.
A grain is a caryopsis- a type of fruit (PO:0009001), while the seed (PO:0009010) is a separate entity, which may be part of the fruit.
Please go through the TO and look at each term with seed in the name:
e.g. TO:0000391 seed size (http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/term_details?term=TO:0000391&session_id=3029amigo1359400529).
- fix is_a parent- should be 'seed anatomy and morphology trait' (TO:0000184), keep other is_a parents for now, except for seed development trait (TO:0000653) - take off that one
- Revise definition using the primary (ie most important) is_a parent as the genus term, refer to PATO etc as we have been doing.
- Add comments where necessary to explain the other is_a parents and other details in existing definition.
- remove the related synonym "related: kernel size" and move it to a narrow synonym of fruit size (TO:0002625)
- open SF tracker for each one and include OBO_SF_TO debxrefs in the OBO file, as always
need a new term seed yield - currently a synonym of grain yield trait, remove that.
There are currently four terms for seed weight:
seed weight TO:0000181:
anatomy and morphology traits
- Continue to restructure terms to follow hierarchy of PO
- Need work:
- Fruit anatomy and morphology trait- see comments on tracker, modify synonymns- I think this is done, no?
- in vitro plant structure anatomy and morphology trait - no child terms exist
- plant cell anatomy and morphology trait - several development traits exist under this category
- plant embryo anatomy and morphology trait - need to work on definitions of child terms (structure is alright)
- portion of plant tissue anatomy and morphology trait - The vascular tissue traits need some work. There is a part_of relation between seed coat color and plant structure anatomy and morphology trait, should this be there?
- Need work:
stress trait
- The two upper level terms here are good
- abiotic stress trait
- Proposed hierarchy:
- environmental stress trait
- temperature stress response trait
- water stress response trait
- radiation stress response trait
- chemical stress response trait
- agricultural practice stress response trait
- environmental stress trait
- Proposed hierarchy:
- abiotic stress trait
- biotic stress trait - these traits have a good structure
biochemical trait
- has some upper level terms that are very good, others just need to become children of the terms that already exist
- terms to keep:
- biological process related trait
- enzymatic activity and protein content related trait (maybe this could be 2 separate traits)
- metabolite content related trait
- mineral and ion content related trait
- terms to keep:
growth and development
- waiting to start the hierarchy until the PO has finished restructuring their growth and development traits
- current PO hierarchy:
- collective plant structure development trait
- plant organ development stage
- plant tissue development stage
- seed development stage
- trichome development stage
- whole plant development stage
- currently in TO there is no upper level structure for this category
yield trait
- should all these terms fall under biomass yield trait?
- e.g. grain yield, harvest index, inflorescence yield, ethanol yield from biomass...all can be children of biomass yield 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
- no terms exist under this category
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
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.
