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:=
+
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]]
 +
  
 
==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]
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[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]
  
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[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]
−
==[https://sourceforge.net/tracker/?func=detail&aid=3495455&group_id=76834&atid=835557 root term: plant trait] (TO:0000387)==
 
−
need to fix definition of plant trait to include cellular components and biochemical traits etc
 
−
 
 
−
current def'n: A measurable or observable characteristic of a plant anatomical entity (PO:0000003) and/or a plant structure development stage (PO:0009012).
 
−
 
 
−
new proposed def'n: A measurable or observable characteristic of a cellular component (GO:0005575), biological process (GO:0008150) or molecular function (GO:0003674) that is part of, or has participant a plant anatomical entity (PO:0000003)and or a plant structure development stage (PO:0009012).
 
  
−
Comment: This includes physiological, molecular and biochemical traits as well.
+
[https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdEQ3dGRmcWEwbXdfUFNSUU4yN25MWlE#gid=0 Rosaceae TO Requests]
  
−
===background on the GO classes:===
+
=Ontology Issues to be worked on:=
−
*cellular component (GO:0005575): The part of a cell or its extracellular environment in which a gene product is located.
 
−
Includes cells and parts of cells like membranes, organelles, symplast, apoplast, plant extracellular matrix (The matrix external to the plant plasma membrane, composed of the cell wall and middle lamella), parts of the pollen wall (exine (including sexine), intine), pollen coat, 
 
  
−
*biological process (GO:0008150): Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
+
=Order of Top Priority sections=
−
Includes: Processes important to plants such as: growth, development, reproduction, senescence, respiration, photosynthesis, metabolism, signaling, response to abiotic (e.g. cold acclimation, vernalization, heat, flooding, drought, response to herbicide, wounding, inorganic substance) and biotic stress (responses to bacteria, fungi, herbivores, insects, viruses, symbionts, defense response, detection of stress, incompatible and compatible responses), rhythmic process (e.g. circadian rhythm > circadian regulation of gene expression), seed development and germination, phloem transport, etc etc..... nitrogen fixation . 
 
  
−
*molecular function (GO:0003674): Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level.
+
'''''***Note: content below needs to be updated***''
−
Includes all the enzyme activities such as catalysis of a biochemical reaction, regulation, binding, nucleic acid binding (transcription factor), receptor activity, transporter activity,etc
+
'''
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3519672&group_id=76834&atid=835557 anatomy and morphology related trait (TO:0000017)]==
+
anatomy and morphology traits
−
current def'n: This category belongs to traits associated with changes in the anatomy or structure of the plant at organ, tissue or cellular level.
+
* 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?
  
−
proposed def'n: A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0000003) or one or more constituent cellular components (GO:0005575) contained therein.
 
  
−
comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010) as well as those of plant anatomical spaces (PO:0025117), portions of plant substance (PO:0025161).
+
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
  
−
''note: The PO ids in the comments do not go into the Dbxrefs''
+
** biotic stress trait - these traits have a good structure
  
−
''may move this stuff to this page: [[anatomy and morphology related trait (TO:0000017)]]''
 
  
 +
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=3519674&group_id=76834&atid=835557 New children of anatomy and morphology related trait (TO:0000017)]===
 
−
This is a valid hierarchy based on the Plant Ontology and will provide a parent for the potato tuber terms requested below.
 
  
−
*new child term and def'n: '''plant organ anatomy and morphology trait''' (TO:0000736): An anatomy and morphology trait (TO:0000017) which is associated with a plant organ (PO:0009008).
+
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
  
−
*new term and def'n: '''plant axis anatomy and morphology trait''' (TO:0000738): plant organ anatomy and morphology trait (TO:0000736) which is associated a plant axis (PO:0025004).
 
  
−
*new child term and def'n: '''shoot axis anatomy and morphology trait''' (TO:0000739): A plant axis trait (TO:0000738) which is associated with a shoot axis (PO:0025029).
+
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.
  
−
*new term and def'n: '''branch anatomy and morphology trait''' (TO:0000740): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with a branch (PO:0025073).
 
  
−
*new term and def'n: '''tuber anatomy and morphology trait ''' (TO:0000741): A branch anatomy and morphology trait (TO:0000740) which is associated with a tuber (PO:0004543).
+
stature and vigor/quality traits
 +
* could these two categories be combine?
  
−
*new term and def'n: '''subterranean tuber anatomy and morphology trait ''' (TO:0000742): A tuber anatomy and morphology trait (TO:0000741) which is associated with a subterranean tuber (PO:0004547).
 
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3519674&group_id=76834&atid=835557 shoot axis anatomy and morphology trait (TO:0000077)]==
+
fertility and sterility traits
−
current def'n: Traits associated with changes in the anatomy or structure of the shoot and its parts.
+
* could we incorporate these to stature and vigor/quality or growth and development?
 +
* There only about 4 traits under this category
  
−
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.
 
  
−
propose new name and def'n:
+
other misc traits
 +
* this trait should be obsoleted
 +
* no terms exist under this category
  
−
'''shoot system anatomy and morphology trait''' (TO:0000077): An anatomy and morphology trait (TO:0000017) which is associated with a shoot system (PO:0009006).
+
=Duplicated terms:=
  
−
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.
+
=[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
  
−
''PO note: look at primary shoot (CPS > shoot system) vs stem (plant organ > plant axis > shoot axis). How can primary shoot be a shoot system?? -needs to be resolved.''
+
and
 +
* stem senescence (TO:0020085) def: "A trait to measure the stem senescence."
 +
is_a: TO:0000654 ! shoot development trait
  
−
''needs updated on OE''
 
  
−
'''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 trait (TO:0000077)''
 
  
−
''Ok''
+
Same problem as before:
  
−
*coleoptile color (plant organ)
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=3531325&group_id=76834&atid=835557 total water soluble content]=
−
*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''
+
* 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
  
−
*relative shoot elongation under submergence (plant organ > plant axis > shoot axis (syn: shoot))
+
and
−
*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''
+
*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
  
−
*hypocotyl length (COP > shoot internode > stem internode > hypocotyl)
+
* inflorescence width (TO:0000637)
−
*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''
+
* inflorescence width (TO:0000804): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the width of an inflorescence (PO:0009049).
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3487511&group_id=76834&atid=835557 tuber traits]==
 
  
−
Terms requested by Syngenta (in bold):
+
* check definition of: TO:0020085 
  
−
'''tuber''' (PO:0004543): An enlarged storage branch (PO:0025073)
+
the term name itself should never be used (except some particular cases) to define a concept...
  
−
probably should be: subterranean tuber (PO:0004547): A tuber (PO:0004543) that is below ground
+
=plant organ anatomy and morphology trait (TO:0000736) and subclasses:=
  
−
'''tuber epidermis''' (PO:0025046): A portion of shoot axis epidermis that is part of a tuber (PO:0004543).
+
=leaf anatomy and morphology trait (TO:0000748)=
−
 
−
probably should be: subterranean tuber epidermis (PO:0025048): A tuber epidermis (PO:0025046) that is part of a subterranean tuber (PO:0004547).
 
  
−
tuber axillary vegetative bud (PO:0025040): An axillary vegetative bud (PO:0004712) that is part of a tuber (PO:0004543). related synonym: '''tuber eye'''
+
Proposed to create two subcategories for leaf a&m trait  
  
−
probably should be: subterranean tuber axillary vegetative bud (PO:0025042): A tuber axillary vegetative bud (PO:0025040) that is part of a subterranean tuber (PO:0004547).
+
*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).
  
−
broad synonym:'''tuber eye'''
+
*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).
  
−
tuber storage parenchyma (PO:0025036): A portion of storage parenchyma (PO:0025035) that is part of a tuber (PO:0004543). exact synonym:'''tuber flesh'''
+
We should also keep general leaf a&m traits such as leaf size to encompass both vascular and non-vascular leaves.
  
−
probably should be: subterranean tuber storage parenchyma (PO:0025038): A portion of tuber storage parenchyma (PO:0025036) that is part of a subterranean tuber (PO:0004547).  
+
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.
  
−
Narrow Synonym: '''potato tuber''' flesh
+
==[https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/271/ specific leaf area]==
  
−
''need to update in PO''
+
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.
  
−
===requested terms and suggested def'ns:===
 
  
−
tuber shape- The shape of the tuber
+
Existing terms:
 +
* name: '''specific leaf area (TO:0000562)''' -is_a: TO:0000540 ! leaf area
  
−
tuber size- The physical size of the tuber
+
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)
  
−
tuber appearance- The overall appearance of the tuber. A 1-9 scale is used, with 1 the lowest score (very poor) and 9 the highest (excellent)
+
Or "A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry mass (TO:New)
  
−
tuber mass- The mass of the tuber
+
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).
  
−
[[File:Tuber.png]]
+
[http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=247869 SLA at Mgdb]
  
−
In the PO: A '''tuber''' is a '''branch''' which is a '''shoot axis''';  shoot axis is_a '''plant_axis'''; which is_a '''plant organ''' part_of the '''shoot system'''
+
* 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.''
  
−
* '''tuber shape'''
+
* mass (PATO:0000125): A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
−
Proposed new term and def'n:
+
* weight (PATO:0000128): A physical quality inhering in a bearer that has mass near a gravitational body.
−
'''subterranean tuber shape''' (TO:0000743): A subterranean tuber anatomy and morphology trait (TO:0000742) which is associated with the shape of a subterranean tuber (PO:0004547).
 
  
−
broad synonym: tuber shape
+
=[https://sourceforge.net/tracker/?func=detail&aid=3520088&group_id=76834&atid=835557 shoot system anatomy and morphology trait] (TO:0000077)=
  
−
refer to PATO shape: PATO:0000052
+
* TO:0020077 : head drop
 +
* TO:0000623 : involucre bristle length
  
−
* '''tuber size'''
+
=Other anatomy and morphology trait classes:=
−
Proposed new term and def'n: '''subterranean tuber size''' (TO:0000744): A subterranean tuber anatomy and morphology trait (TO:0000742) which is associated with the size of a subterranean tuber (PO:0004547).
 
  
−
refer to PATO size: PATO:0000117
+
==cell organelle structure trait (TO:0002713)==
−
 
 
−
broad synonym: tuber size
 
−
 
 
−
* '''tuber appearance'''
 
−
Proposed new term and def'n: '''subterranean tuber appearance''' (TO:0000745): A subterranean tuber anatomy and morphology trait (TO:0000742) which is associated with the appearance of a subterranean tuber (PO:0004547).
 
−
 
 
−
comment: A 1-9 scale is used to score the overall appearance of the tuber, with 1 the lowest score (very poor) and 9 the highest (excellent)
 
−
 
 
−
broad synonym: tuber appearance
 
−
 
 
−
No PATO reference for refer to appearance
 
−
 
 
−
* '''tuber mass'''
 
−
Proposed new term and def'n: '''subterranean tuber mass''' (TO:0000746): A subterranean tuber anatomy and morphology trait (TO:0000742) which is associated with the mass of a subterranean tuber (PO:0004547).
 
−
 
 
−
broad synonym: tuber mass
 
−
 
 
−
refer to PATO mass: PATO:0000125
 
−
 
 
−
''done: 4-20-12''
 
−
 
 
−
 
 
−
 
 
−
==[https://sourceforge.net/tracker/?func=detail&aid=3520729&group_id=76834&atid=835557 root anatomy and morphology trait (TO:0000043)]==
 
−
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).
 
−
 
 
−
 
 
−
''make a child of the new class: plant axis anatomy and morphology trait (TO:0000738)''
 
−
 
 
−
root (PO:0025025): A plant axis that is part of a root system. [source: POC:curators]
 
−
 
 
−
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.
 
−
 
 
−
PO hierarchy: plant organ > plant axis > shoot axis > root
 
−
 
 
−
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.''
 
−
 
 
−
==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 related trait (TO:0000017)
 
−
 
 
−
>collective plant structure anatomy and morphology related trait (proposed)
 
−
 
 
−
>>fruit anatomy and morphology related 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 related 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 280: 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]]
−
 
 
−
===whole plant trait TO:0000398===
 
−
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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