Difference between revisions of "Plant Trait Ontology"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(99 intermediate revisions by 2 users not shown)
Line 7: Line 7:
 
=New:=
 
=New:=
  
−
Link to [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/browse.cgi?session_id=9762amigo1337275750 AMIGO TO Browser]....under development!
+
Link to [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi AMIGO TO-Dev Browser]....under development!
  
−
=Upcoming Presentations and Publications=
+
New tiny URL: http://tinyurl.com/Plant-Trait-Ontology
  
−
Call for papers: [http://www.keod.ic3k.org/CallForPapers.aspx Knowledge Engineering and Ontology Development]
+
DBx Ref Reminder: use "TO_GIT " for links to GitHub
 +
 
 +
 
 +
HTML code for graph editor: Click "edit" to see
 +
 
 +
Display IDs:<center>$name$<br><font size=-1>$id$</font></center>
 +
 
 +
ID Manger settings: TO:$sequence(7,0000001,0020000)$
 +
 
 +
=Presentations and Publications=
 +
[http://www.keod.ic3k.org/CallForPapers.aspx Knowledge Engineering and Ontology Development]
  
 
[https://docs.google.com/document/d/1hQyWohPtai3BlB9NNYW4o9bTQH0RyWjf2cWVuXOcxBc/edit Crop Plant Trait Ontology paper]
 
[https://docs.google.com/document/d/1hQyWohPtai3BlB9NNYW4o9bTQH0RyWjf2cWVuXOcxBc/edit Crop Plant Trait Ontology paper]
−
 
−
Also: [http://ktw.mimos.my/aos2012/ Ontologies and semantic technologies for agricultural knowledge in practice]
 
  
 
=Related Wiki Pages and Links:=
 
=Related Wiki Pages and Links:=
Line 21: Line 29:
 
Link to [http://www.gramene.org/plant_ontology/ontology_browse.html#to TO on Gramene]
 
Link to [http://www.gramene.org/plant_ontology/ontology_browse.html#to TO on Gramene]
  
−
Details about the plans for the [[Crop_Ontology_Workshop_at_OSU,_2012]]
+
Details about the [[Crop_Ontology_Workshop_at_OSU,_2012]]
  
 
Work on the wood traits: [[Goal_3._Wood_qualities_and_phenotypes]]
 
Work on the wood traits: [[Goal_3._Wood_qualities_and_phenotypes]]
  
−
[http://sourceforge.net/tracker/?group_id=76834&atid=835557 TO Tracker] on SourceForge
+
[https://github.com/Planteome/plant-trait-ontology/issues TO Issue Tracker] on GitHub
  
 
Trait Ontology on Bioportal:  [http://bioportal.bioontology.org/ontologies/1037 TO]
 
Trait Ontology on Bioportal:  [http://bioportal.bioontology.org/ontologies/1037 TO]
  
 
Go here for more info on [[Changes to the TO- Spring 2012]]
 
Go here for more info on [[Changes to the TO- Spring 2012]]
 +
  
 
==Links to Collaborator Sites:==
 
==Links to Collaborator Sites:==
 +
 +
[http://www.cropontology.org/ Crop Ontology Site]
  
 
[http://www.cropontology.org/ GCP Phenotype and Trait Ontology]
 
[http://www.cropontology.org/ GCP Phenotype and Trait Ontology]
Line 43: Line 54:
 
[http://triticeaetoolbox.org/barley/ Triticeae Toolbox Barley]
 
[http://triticeaetoolbox.org/barley/ Triticeae Toolbox Barley]
  
−
[http://triticeaetoolbox.org/wheat/traits.php Trait Descriptions]
+
[http://triticeaetoolbox.org/wheat/traits.php T3 Trait Descriptions]
  
−
Grin Global project - Peter Bretting, David Okomuri
+
[http://www.grin-global.org/index.php/Main_Page Grin Global] project - Peter Bretting, David Okamura
  
 
=Trait lists on Google docs=
 
=Trait lists on Google docs=
 +
[https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdEY0YmY0LUlpMVdyZFBSQlVFb0gwSnc#gid=0 cowpea TO sheet]
 +
 
[https://docs.google.com/spreadsheet/ccc?key=0AlNkypVaksxGdF85YlJRSjZUaG9HMnJvQVYyVm1Qbmc Wood Traits]
 
[https://docs.google.com/spreadsheet/ccc?key=0AlNkypVaksxGdF85YlJRSjZUaG9HMnJvQVYyVm1Qbmc Wood Traits]
  
Line 56: Line 69:
 
[https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdExrLWlPVWpWZm5BMzJycUhuYWR0Vmc#gid=0 Bioenergy Traits]
 
[https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdExrLWlPVWpWZm5BMzJycUhuYWR0Vmc#gid=0 Bioenergy Traits]
  
−
=Ontology Issues to be worked on:=
+
[https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc#gid=8 CROP Workshop Trait List]
−
=Duplicated terms:=
 
−
* stem senescence (TO:0001036) def: "A measurement of aging of stem."
 
−
is_a: TO:0000361 ! stem anatomy and morphology trait
 
  
−
and
+
[https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdEQ3dGRmcWEwbXdfUFNSUU4yN25MWlE#gid=0 Rosaceae TO Requests]
−
* stem senescence (TO:0020085) def: "A trait to measure the stem senescence."
 
−
is_a: TO:0000654 ! shoot development trait
 
  
 +
=Ontology Issues to be worked on:=
  
 +
=Order of Top Priority sections=
  
−
Same problem as before:
+
'''''***Note: content below needs to be updated***''
 +
'''
  
−
* total water soluble content (TO:0002711): def: "The concentration of water soluble components in the plant as determined by refractive index."
+
anatomy and morphology traits
−
is_a: TO:0000281 ! metabolite content related trait
+
* Continue to restructure terms to follow hierarchy of PO
 +
** Need work:
 +
*** [https://sourceforge.net/tracker/?func=detail&aid=3544697&group_id=76834&atid=835557 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?
  
−
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."
+
stress trait
−
comment: This trait is usually highly correlated with total soluble sugar content (TO:0000340). Often determined in fresh tissue.
+
* The two upper level terms here are good
−
synonym: "total dissolved solids content" EXACT []
+
** abiotic stress trait
−
is_a: TO:0000281 ! metabolite content related 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  
  
 +
** biotic stress trait - these traits have a good structure
  
−
* check definition of: TO:0020085 
 
  
−
the term name itself should never be used (except some particular cases) to define a concept...
+
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
  
−
=[https://sourceforge.net/tracker/?func=detail&aid=3521773&group_id=76834&atid=835557 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
+
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
  
−
Also includes:
 
−
* parts of [http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0009010&session_id=6555b1335805655 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): ,
+
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.
  
−
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:
+
stature and vigor/quality traits
−
* 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).
+
* could these two categories be combine?
  
−
''completed''
 
  
 +
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
  
  
−
=plant organ anatomy and morphology trait (TO:0000736) and subclasses:=
+
other misc traits
 +
* this trait should be obsoleted
 +
* no terms exist under this category
  
−
==shoot axis anatomy and morphology trait (TO:0000739)==
+
=Duplicated terms:=
  
−
* inflorescence axis anatomy and morphology trait (TO:0000782): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with an inflorescence axis (PO:0020122).
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=3531323&group_id=76834&atid=835557 stem senescence]=
 +
* stem senescence (TO:0001036) def: "A measurement of aging of stem."
 +
is_a: TO:0000361 ! stem anatomy and morphology trait
  
−
**inflorescence branch anatomy and morphology trait (TO:xxxxxxx): A inflorescence axis anatomy and morphology trait (TO:0000782) which is associated with an inflorescence branch (PO:ID).
+
and
 +
* stem senescence (TO:0020085) def: "A trait to measure the stem senescence."
 +
is_a: TO:0000654 ! shoot development trait
  
−
***tassel branch anatomy and morphology trait (TO:xxxxxxx): An inflorescence branch anatomy and morphology trait (TO:xxxxxxx) which is associated with a tassel branch (PO:ID)
 
  
−
===User requests:===
 
−
* tassel type: Branching type of tassel whether primary or primary-secondary or primary-secondary- tertiary
 
−
* Tassel branches dry weight: The dry weight of tassel branches (grams) just prior to pollen shed.
 
−
 
−
* Tassel branches number: Number of branches of tassel
 
−
 
  
−
'''Other existing shoot axis classes:'''
+
Same problem as before:
  
−
*stem anatomy and morphology trait (plant organ > plant axis > shoot axis > stem)
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=3531325&group_id=76834&atid=835557 total water soluble content]=
  
−
*relative shoot elongation under submergence (plant organ > plant axis > shoot axis (syn: shoot))
+
* 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
  
−
*shootless (plant organ > plant axis > shoot axis (syn: shoot))
+
and
  
−
*shoot habit (plant organ > plant axis > shoot axis (syn: shoot))
+
*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
  
−
*tiller angle (plant organ > plant axis > shoot axis >shoot-borne shoot system> axillary shoot system >basal axillary shoot (syn: tiller))
+
* inflorescence width (TO:0000637)
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3527677&group_id=76834&atid=835557 user requested: peduncle traits]==
+
* inflorescence width (TO:0000804): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the width of an inflorescence (PO:0009049).
−
plant structure > plant organ > plant_axis >shoot axis > peduncle
 
  
−
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.
+
* check definition of: TO:0020085  
  
 +
the term name itself should never be used (except some particular cases) to define a concept...
  
−
parent: shoot axis anatomy and morphology trait (TO:0000739): A plant axis trait (TO:0000738) which is associated with a shoot axis (PO:0025029).
+
=plant organ anatomy and morphology trait (TO:0000736) and subclasses:=
−
 
 
−
'''New term: peduncle anatomy and morphology trait (TO:0000776):''' 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:0000776) which is associated with a visual observation of the presence of cuticular wax (PO:0025386).
+
=leaf anatomy and morphology trait (TO:0000748)=
  
−
No PATO term for waxiness- suggested new term on SF. suggested definitions: the state or quality of being waxy or the presence of long chain aliphatic lipids on the surface of an organism.
+
Proposed to create two subcategories for leaf a&m trait 
  
−
see related PO terms: 
+
*vascular leaf anatomy and morphology trait (TO:0000419): A leaf anatomy and morphology trait (TO:0000748) which is associated with a vascular leaf (PO:0009025).
−
*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.
 
  
−
Moved existing terms to new parent and redefined:  
+
*non-vascular leaf anatomy and morphology trait (TO:0000925): A leaf anatomy and morphology trait (TO:0000748) which is associated with a non-vascular leaf (PO:0025075).
  
−
* peduncle length (TO:0002691): A peduncle anatomy and morphology trait (TO:0000776) which is associated with the length of a peduncle (PO:0009053). Refer to length (PATO:0000122)
+
We should also keep general leaf a&m traits such as leaf size to encompass both vascular and non-vascular leaves.
−
* peduncle width (TO:0000649): A peduncle anatomy and morphology trait (TO:0000776) which is associated with the width of a peduncle (PO:0025386). Refer to width (PATO:0000921)
 
−
* peduncle top diameter (TO:0000546): A peduncle anatomy and morphology trait (TO:0000776) which is associated with the diameter at the tip of the peduncle (PO:0009053). Refer to diameter (PATO:0001334)
 
  
−
''completed''
+
Need to add comment to all general leaf terms: If you are annotating to this term, please add an additional annotation to vascular leaf anatomy and morphology (TO:0000419) or non-vascular leaf anatomy and morphology trait (TO:0000925), depending on the species.
  
−
see also: TO:0000545 : panicle base to lowest branch: "peduncle length from panicle base to first primary branch" [related synonym]
+
==[https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/271/ specific leaf area]==
  
−
=[https://sourceforge.net/tracker/?func=detail&aid=3520088&group_id=76834&atid=835557 shoot system anatomy and morphology trait] (TO:0000077)=
+
Request from SF: Specific leaf area
−
We may eventually want to introduce a collective plant system anatomy and morphology trait (TO:xxxxxxx) as a parent term.''
+
* definition: leaf area measured in ratio to leaf dry mass.
 +
* synonym: leaf specific area
 +
* might need addition of 'leaf dry mass' as new trait.
  
−
'''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.
+
Existing terms:
 +
* name: '''specific leaf area (TO:0000562)''' -is_a: TO:0000540 ! leaf area
  
−
''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.''
+
Proposed definition: A leaf area (TO:0000540) trait that is the ratio of the leaf area (TO:0000540) to the leaf dry weight (TO:0001014)
  
−
Subclasses:
+
Or "A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry mass (TO:New)
  
−
Need new sub-class: '''reproductive shoot system anatomy and morphology trait (TO:xxxxxxx):''' A shoot system anatomy and morphology trait (TO:0000077) that is associated with an reproductive shoot system (PO:0025082).
+
Or use both: A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry weight (TO:0001014) or leaf dry mass (TO:New).
  
−
'''*inflorescence anatomy and morphology trait (TO:0000373):''' (CPS > shoot system > reproductive shoot system > inflorescence)
+
[http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=247869 SLA at Mgdb]
  
−
current def'n: Traits associated with changes in the anatomy or structure of the inflorescence and its parts.
+
* leaf weight (TO:0000505)  def: "A leaf anatomy and morphology trait (TO:0000505) which is associated with the measure of leaf weight."
 +
**leaf wet weight id: TO:0000891  def: "A leaf weight trait (TO:0000505) which is associated with the measure of the wet weight of a leaf (PO:0025034)." [PO:0025034, TO:moorel]
 +
**leaf dry weight  id: TO:0001014 def: "A leaf weight trait (TO:0000505) which is associated with the measure of the dry weight of a leaf (PO:0025034)." [GR:pj, PO:0025034, TO:moorel]
  
−
new def'n: inflorescence anatomy and morphology trait: A reproductive shoot system anatomy and morphology trait (TO:xxxxxxx) that is associated with an inflorescence (PO:0009049).
+
''Need to add references to PATO weight in these.''
  
−
Need new sub-class: '''tassel inflorescence anatomy and morphology trait (TO:xxxxxxx):'''An inflorescence anatomy and morphology trait (TO:0000373) that is associated with an inflorescence (PO:0020126).
+
* mass (PATO:0000125): A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
−
+
* weight (PATO:0000128): A physical quality inhering in a bearer that has mass near a gravitational body.
  
 +
=[https://sourceforge.net/tracker/?func=detail&aid=3520088&group_id=76834&atid=835557 shoot system anatomy and morphology trait] (TO:0000077)=
  
−
 
+
* TO:0020077 : head drop
−
*'''flower anatomy and morphology trait ''' (CPS > shoot system > reproductive shoot system > flower):
+
* TO:0000623 : involucre bristle length
−
New def'n: A reproductive shoot system anatomy and morphology trait (TO:xxxxxxx) that is associated with an flower (PO:xxxxxxx).
 
−
 
 
−
=other=
 
−
 
 
−
 
 
−
 
 
−
 
 
−
* [https://sourceforge.net/tracker/?func=detail&aid=3525909&group_id=76834&atid=835557 plant color] (TO:0000708): - move to 'stature and vigor trait'
 
−
Current def'n: The color of the plant.
 
−
 
 
−
new def'n: A stature and vigor trait (TO:0000133) which is associated with the color of a plant. Refer to color PATO:0000014.
 
−
 
 
−
 
 
−
*[https://sourceforge.net/tracker/?func=detail&aid=3525898&group_id=76834&atid=835557 plant height] (TO:0000207): has two is_a parents: 'shoot system anatomy and morphology trait' ; 'stature and vigor trait'
 
−
- this should just be a "stature and vigor trait, rather than keeping it in the Anatomy and Morphology hierarchy as well..
 
−
 
 
−
Current def'n: Actual measurement of plant height from soil surface to the highest point in plant as identified in the study.
 
−
 
 
−
new def'n: A stature and vigor trait (To:0000133) which is associated with the height of a plant. Refer to height PATO:0000119.
 
−
 
 
−
''completed''
 
−
 
 
−
==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:=
 
=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)==
 
==cell organelle structure trait (TO:0002713)==
Line 260: Line 233:
  
 
*plastid development trait
 
*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
 
  
 
==vascular tissue related trait==
 
==vascular tissue related trait==

Latest revision as of 21:44, 29 January 2016

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-Dev Browser....under development!

New tiny URL: http://tinyurl.com/Plant-Trait-Ontology

DBx Ref Reminder: use "TO_GIT " for links to GitHub


HTML code for graph editor: Click "edit" to see

Display IDs:

$name$
$id$

ID Manger settings: TO:$sequence(7,0000001,0020000)$

Presentations and Publications

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 Issue Tracker on GitHub

Trait Ontology on Bioportal: TO

Go here for more info on Changes to the TO- Spring 2012


Links to Collaborator Sites:

Crop Ontology Site

GCP Phenotype and Trait Ontology

Sol Genomics Network

SoyBase

Triticeae Toolbox

Triticeae Toolbox Barley

T3 Trait Descriptions

Grin Global project - Peter Bretting, David Okamura

Trait lists on Google docs

cowpea TO sheet

Wood Traits

Crop Traits List

Triticeae Toolbox Traits for Wheat

Bioenergy Traits

CROP Workshop Trait List

Rosaceae TO Requests

Ontology Issues to be worked on:

Order of Top Priority sections

***Note: content below needs to be updated***

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?


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
    • 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


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:

leaf anatomy and morphology trait (TO:0000748)

Proposed to create two subcategories for leaf a&m trait

  • vascular leaf anatomy and morphology trait (TO:0000419): A leaf anatomy and morphology trait (TO:0000748) which is associated with a vascular leaf (PO:0009025).
  • non-vascular leaf anatomy and morphology trait (TO:0000925): A leaf anatomy and morphology trait (TO:0000748) which is associated with a non-vascular leaf (PO:0025075).

We should also keep general leaf a&m traits such as leaf size to encompass both vascular and non-vascular leaves.

Need to add comment to all general leaf terms: If you are annotating to this term, please add an additional annotation to vascular leaf anatomy and morphology (TO:0000419) or non-vascular leaf anatomy and morphology trait (TO:0000925), depending on the species.

specific leaf area

Request from SF: Specific leaf area

  • definition: leaf area measured in ratio to leaf dry mass.
  • synonym: leaf specific area
  • might need addition of 'leaf dry mass' as new trait.


Existing terms:

  • name: specific leaf area (TO:0000562) -is_a: TO:0000540 ! leaf area

Proposed definition: A leaf area (TO:0000540) trait that is the ratio of the leaf area (TO:0000540) to the leaf dry weight (TO:0001014)

Or "A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry mass (TO:New)

Or use both: A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry weight (TO:0001014) or leaf dry mass (TO:New).

SLA at Mgdb

  • leaf weight (TO:0000505) def: "A leaf anatomy and morphology trait (TO:0000505) which is associated with the measure of leaf weight."
    • leaf wet weight id: TO:0000891 def: "A leaf weight trait (TO:0000505) which is associated with the measure of the wet weight of a leaf (PO:0025034)." [PO:0025034, TO:moorel]
    • leaf dry weight id: TO:0001014 def: "A leaf weight trait (TO:0000505) which is associated with the measure of the dry weight of a leaf (PO:0025034)." [GR:pj, PO:0025034, TO:moorel]

Need to add references to PATO weight in these.

  • mass (PATO:0000125): A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
  • weight (PATO:0000128): A physical quality inhering in a bearer that has mass near a gravitational body.

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

vascular tissue related 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.

Retrieved from "http://wiki.plantontology.org/index.php?title=Plant_Trait_Ontology&oldid=26240"