Difference between revisions of "Plant Trait Ontology"

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This page will be a place to keep track of the work on developing the Plant Trait Ontology
 
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:=
 
=New:=
  
−
Call for papers: [http://www.keod.ic3k.org/CallForPapers.aspx Knowledge Engineering and Ontology Development]
+
Link to [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi 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:<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 15: 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 37: 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 50: 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:=
+
[https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc#gid=8 CROP Workshop Trait List]
−
=plant organ anatomy and morphology traits (TO:0000736)=
 
−
* [https://sourceforge.net/tracker/?func=detail&aid=3521426&group_id=76834&atid=835557 phyllome anatomy and morphology trait (TO:0000747)]
 
−
 
 
−
PO 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:0000747):''' A plant organ anatomy and morphology trait (TO:0000736) which is associated with a phyllome (PO:0006001).
 
  
−
* existing class: '''leaf anatomy and morphology trait (TO:0000419):''' Traits associated with changes in the anatomy or structure of the leaf and its parts.
+
[https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdEQ3dGRmcWEwbXdfUFNSUU4yN25MWlE#gid=0 Rosaceae TO Requests]
  
−
this refers only to vascular leaves, there are 625 annotations on Gramene for this class
+
=Ontology Issues to be worked on:=
  
−
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.
+
=Order of Top Priority sections=
  
−
* new term: '''leaf anatomy and morphology trait (TO:0000748)''': A phyllome anatomy and morphology trait (TO:0000747) which is associated with a leaf (PO:0025034).
+
'''''***Note: content below needs to be updated***''
−
+
'''
−
*'''vascular leaf anatomy and morphology trait (TO:0000419):''' revised def'n: A leaf anatomy and morphology trait (TO:0000748) which is associated with a vascular leaf (PO:0009025).
 
  
−
*'''cotyledon anatomy and morphology trait (TO:0000749):''' A vascular leaf anatomy and morphology trait (TO:0000419) which is associated with a cotyledon (PO:0020030).
+
anatomy and morphology traits
 +
* 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?
  
−
==Requested [https://sourceforge.net/tracker/?func=detail&aid=3521436&group_id=76834&atid=835557 cotyledon trait terms]:==
 
−
From: Syngenta (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
 
  
 +
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
  
−
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).
+
** biotic stress trait - these traits have a good structure
  
−
* cotyledon color(TO:0000750):  A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the shape of a cotyledon(PO:0020030).
 
−
refer to PATO shape: PATO:0000052
 
  
−
* cotyledon number (TO:0000751): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the number of cotyledons (PO:0020030).
+
biochemical trait
−
refer to PATO count: PATO:0000070
+
* 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
  
−
* cotyledon size (TO:0000752): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the size of a cotyledon(PO:0020030).
 
−
refer to PATO size: PATO:0000117
 
  
−
===coleoptile trait terms===
+
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
  
−
PO hierarchy:  plant organ > coleoptile >embryo coleoptile (PO:00252860 and seedling coleoptile (PO:0025287)
 
  
−
Existing TO terms:
+
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.
  
−
* coleoptile color (TO:0000244) def: "Measure of color of the coleoptile in the germinating seedling." [GR:pj]
 
−
synonym: "COLCL" RELATED
 
  
−
is_a: TO:0000064 ! embryo related trait
+
stature and vigor/quality traits
 +
* could these two categories be combine?
  
−
is_a: TO:0000736 ! plant organ anatomy and morphology trait
 
  
 +
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
  
  
−
* coleoptile length (TO:0001007) def: "Measurement of the length of the coleoptile in the germinating seed." [GR:pj]
+
other misc traits
 +
* this trait should be obsoleted
 +
* no terms exist under this category
  
−
is_a: TO:0000736 ! plant organ anatomy and morphology trait
+
=Duplicated terms:=
  
−
Need new class: coleoptile anatomy and morphology trait (TO:0001007): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).
+
=[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
  
−
=cardinal organ part anatomy and morphology traits (TO:xxxxxx)=
+
and
−
''this section is in progress....''
+
* stem senescence (TO:0020085) def: "A trait to measure the stem senescence."
 +
is_a: TO:0000654 ! shoot development trait
  
−
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,  seed (hilum (PO:0020063), hilum groove (PO:0004719)????), archegonium, fruit, ovary, palea, petiole, etc etc
 
  
−
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:  
+
Same problem as before:
−
* cardinal organ part anatomy and morphology trait (TO:xxxxxx): An anatomy and morphology trait (TO:0000017) which is associated with a cardinal organ part (PO:id).
 
  
−
==stem internode traits: ==
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=3531325&group_id=76834&atid=835557 total water soluble content]=
−
PO hierarchy: cardinal organ part > shoot internode > stem internode > hypocotyl (PO:0020100), mesocotyl (PO:0020037) and epicotyl (PO:0020035)
 
  
−
* shoot internode anatomy and morphology trait (TO:xxxxxx): ''fill in def'n''
+
* 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
  
−
* stem internode anatomy and morphology trait (TO:xxxxxx): ''fill in def'n''
+
and
  
−
* hypocotyl anatomy and morphology trait (TO:xxxxxx): ''fill in def'n''
+
*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
  
−
* mesocotyl anatomy and morphology trait (TO:xxxxxx): ''fill in def'n''
+
* 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).
  
−
Existing TO terms: these are currently children of ''shoot system anatomy and morphology trait''
 
  
−
* hypocotyl length (TO:xxxxxx): A hypocotyl anatomy and morphology trait (TO:xxxxxx)... ''fill in def'n''
+
* check definition of: TO:0020085 
  
−
* mesocotyl length (TO:xxxxxx): A mesocotyl anatomy and morphology trait (TO:xxxxxx)..''fill in def'n''
+
the term name itself should never be used (except some particular cases) to define a concept...
  
−
===user requested hypocotyl color===
+
=plant organ anatomy and morphology trait (TO:0000736) and subclasses:=
−
From: Syngenta (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
 
  
−
* hypocotyl color
+
=leaf anatomy and morphology trait (TO:0000748)=
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3520729&group_id=76834&atid=835557 root anatomy and morphology trait (TO:0000043)]==
+
Proposed to create two subcategories for leaf a&m trait
−
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).
+
*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).
  
−
''make a child of the new class: plant axis anatomy and morphology trait (TO:0000738)''
+
We should also keep general leaf a&m traits such as leaf size to encompass both vascular and non-vascular leaves.
  
−
root (PO:0025025): A plant axis that is part of a root system. [source: POC:curators]
+
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.
  
−
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.
+
==[https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/271/ specific leaf area]==
  
−
PO hierarchy: plant organ > plant axis > shoot axis > root
+
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.
  
−
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.''
+
Existing terms:
 +
* name: '''specific leaf area (TO:0000562)''' -is_a: TO:0000540 ! leaf area
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3520088&group_id=76834&atid=835557 shoot system anatomy and morphology trait] (TO:0000077)==
+
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)
−
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.
+
Or "A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry mass (TO:New)
  
−
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).
+
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).
  
−
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.
+
[http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=247869 SLA at Mgdb]
  
−
''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.''
+
* 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]
  
−
===Reassigning the child classes===
+
''Need to add references to PATO weight in these.''
−
'''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)''
 
  
 +
* 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.
  
−
*coleoptile color (plant organ)
+
=[https://sourceforge.net/tracker/?func=detail&aid=3520088&group_id=76834&atid=835557 shoot system anatomy and morphology trait] (TO:0000077)=
−
*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''
+
* TO:0020077 : head drop
 +
* TO:0000623 : involucre bristle length
  
−
*relative shoot elongation under submergence (plant organ > plant axis > shoot axis (syn: shoot))
+
=Other anatomy and morphology trait classes:=
−
*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''
+
==cell organelle structure trait (TO:0002713)==
−
 
 
−
*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).   
 
Need to resolve whether this is an anatomy and morphology related trait (TO:0000017) or a growth and development trait (TO:0000357).   
  
Line 255: Line 234:
 
*plastid development trait
 
*plastid development trait
  
−
===seed anatomy and morphology trait (TO:0000184)===
+
==vascular tissue related trait==
 +
 +
==new term plant aspect (TO:0000737)==  
  
−
current def'n: Traits associated with changes in the anatomy or structure of the seed and its parts.
+
Should this go under stature or vigor trait (TO:0000133)? - refers to a whole plant
  
−
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]
+
==whole plant trait TO:0000398==
−
 
+
has been obsoleted, maybe we should consider bringing back?
−
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)
+
==Other top level classes:==
−
*endosperm related trait
+
===growth and development trait===
−
*seed coat color
+
growth and development trait (TO:0000357): Traits associated with observing effects on the development of the plant or plant parts.
−
*seed color
 
−
*seed shape
 
−
*seed texture
 
  
−
===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
+
[[Category:Collaborations]]
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===whole plant trait TO:0000398===
 
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has been obsoleted, maybe we should consider bringing back?
 

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.

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