Difference between revisions of "Plant Trait Ontology"

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=New:=
 
=New:=
  
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Link to [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi AMIGO TO Browser]....under development!
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Link to [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi AMIGO TO-Dev Browser]....under development!
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New tiny URL: http://tinyurl.com/Plant-Trait-Ontology
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DBx Ref Reminder: use "TO_GIT " for links to GitHub
  
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DBx Ref Reminder: use "OBO_SF_TO" not "OBO_SF_ID" for links to SourceForge
 
  
 
HTML code for graph editor: Click "edit" to see
 
HTML code for graph editor: Click "edit" to see
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ID Manger settings: TO:$sequence(7,0000001,0020000)$
 
ID Manger settings: TO:$sequence(7,0000001,0020000)$
  
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=Upcoming Presentations and Publications=
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=Presentations and Publications=
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[http://www.keod.ic3k.org/CallForPapers.aspx Knowledge Engineering and Ontology Development]
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Call for papers: [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]
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Work on the wood traits: [[Goal_3._Wood_qualities_and_phenotypes]]
 
Work on the wood traits: [[Goal_3._Wood_qualities_and_phenotypes]]
  
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[http://sourceforge.net/tracker/?group_id=76834&atid=835557 TO Tracker] on SourceForge
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[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]]
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==Links to Collaborator Sites:==
 
==Links to Collaborator Sites:==
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[http://www.cropontology.org/ Crop Ontology Site]
 
[http://www.cropontology.org/ Crop Ontology Site]
  
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[https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc#gid=8 CROP Workshop Trait List]
 
[https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc#gid=8 CROP Workshop Trait List]
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[https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdEQ3dGRmcWEwbXdfUFNSUU4yN25MWlE#gid=0 Rosaceae TO Requests]
  
 
=Ontology Issues to be worked on:=
 
=Ontology Issues to be worked on:=
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=Order of Top Priority sections=
 
=Order of Top Priority sections=
  
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'''For the week of Jan 28th to Feb 1st:'''
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'''''***Note: content below needs to be updated***''
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'''
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We have to sort out the mixed up terms concerning grains and seeds.
 
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A grain is a caryopsis- a type of fruit (PO:0009001), while the seed (PO:0009010) is a separate entity, which may be part of the fruit.
 
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Please go through the TO and look at each term with seed in the name:
 
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e.g. TO:0000391 seed size (http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/term_details?term=TO:0000391&session_id=3029amigo1359400529).
 
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- fix is_a parent- should be 'seed anatomy and morphology trait' (TO:0000184), keep other is_a parents for now, except for seed development trait (TO:0000653) - take off that one
 
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- Revise definition using the primary (ie most important) is_a parent as the genus term, refer to PATO etc as we have been doing.
 
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- Add comments where necessary to explain the other is_a parents and other details in existing definition.
 
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- remove the related synonym "related: kernel size" and move it to a narrow synonym of fruit size (TO:0002625)
 
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- open SF tracker for each one and include OBO_SF_TO debxrefs in the OBO file, as always
 
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need a new term seed yield - currently a synonym of grain yield trait, remove that.
 
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---
 
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Seed size and seed shape should be different trackers
 
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------
 
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There are currently four terms for ''seed weight'':
 
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seed weight TO:0000181:
 
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anatomy and morphology traits
 
anatomy and morphology traits
 
* Continue to restructure terms to follow hierarchy of PO
 
* Continue to restructure terms to follow hierarchy of PO
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=plant organ anatomy and morphology trait (TO:0000736) and subclasses:=
 
=plant organ anatomy and morphology trait (TO:0000736) and subclasses:=
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=leaf anatomy and morphology trait (TO:0000748)=
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Proposed to create two subcategories for leaf a&m trait 
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*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).
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*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).
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We should also keep general leaf a&m traits such as leaf size to encompass both vascular and non-vascular leaves.
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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.
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==[https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/271/ specific leaf area]==
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Request from SF:  Specific leaf area
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* definition: leaf area measured in ratio to leaf dry mass.
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* synonym: leaf specific area
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* might need addition of 'leaf dry mass' as new trait.
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Existing terms:
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* name: '''specific leaf area (TO:0000562)''' -is_a: TO:0000540 ! leaf area
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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)
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Or "A leaf area trait (TO:0000540) that is the ratio of the leaf area (TO:0000540) to the leaf dry mass (TO:New)
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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).
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[http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=247869 SLA at Mgdb]
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* leaf weight (TO:0000505)  def: "A leaf anatomy and morphology trait (TO:0000505) which is associated with the measure of leaf weight."
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**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]
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**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]
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''Need to add references to PATO weight in these.''
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* mass (PATO:0000125): A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
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* 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)=
 
=[https://sourceforge.net/tracker/?func=detail&aid=3520088&group_id=76834&atid=835557 shoot system anatomy and morphology trait] (TO:0000077)=

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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