Difference between revisions of "Plant Trait Ontology"
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− | Link to [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi 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! |
− | + | 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] | ||
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− | |||
=Related Wiki Pages and Links:= | =Related Wiki Pages and Links:= | ||
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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 | + | 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]] | ||
− | [ | + | [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] | ||
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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 | + | [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=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc#gid=8 CROP Workshop Trait List] | [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc#gid=8 CROP Workshop Trait List] | ||
+ | |||
+ | [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= | ||
− | anatomy and morphology | + | '''''***Note: content below needs to be updated***'' |
+ | ''' | ||
+ | |||
+ | anatomy and morphology traits | ||
* Continue to restructure terms to follow hierarchy of PO | * Continue to restructure terms to follow hierarchy of PO | ||
** Need work: | ** 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 | *** 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 cell anatomy and morphology trait - several development traits exist under this category | ||
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=plant organ anatomy and morphology trait (TO:0000736) and subclasses:= | =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. | ||
+ | |||
+ | ==[https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/271/ 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). | ||
+ | |||
+ | [http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=247869 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. | ||
=[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:
$id$
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:
GCP Phenotype and Trait Ontology
Grin Global project - Peter Bretting, David Okamura
Trait lists on Google docs
Triticeae Toolbox Traits for Wheat
Ontology Issues to be worked on:
Order of Top Priority sections
***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?
- Need work:
stress trait
- The two upper level terms here are good
- abiotic stress trait
- Proposed hierarchy:
- environmental stress trait
- temperature stress response trait
- water stress response trait
- radiation stress response trait
- chemical stress response trait
- agricultural practice stress response trait
- environmental stress trait
- Proposed hierarchy:
- abiotic stress trait
- biotic stress trait - these traits have a good structure
biochemical trait
- has some upper level terms that are very good, others just need to become children of the terms that already exist
- terms to keep:
- biological process related trait
- enzymatic activity and protein content related trait (maybe this could be 2 separate traits)
- metabolite content related trait
- mineral and ion content related trait
- terms to keep:
growth and development
- waiting to start the hierarchy until the PO has finished restructuring their growth and development traits
- current PO hierarchy:
- collective plant structure development trait
- plant organ development stage
- plant tissue development stage
- seed development stage
- trichome development stage
- whole plant development stage
- currently in TO there is no upper level structure for this category
yield trait
- should all these terms fall under biomass yield trait?
- e.g. grain yield, harvest index, inflorescence yield, ethanol yield from biomass...all can be children of biomass yield trait.
stature and vigor/quality traits
- could these two categories be combine?
fertility and sterility traits
- could we incorporate these to stature and vigor/quality or growth and development?
- There only about 4 traits under this category
other misc traits
- this trait should be obsoleted
- no terms exist under this category
Duplicated terms:
stem senescence
- stem senescence (TO:0001036) def: "A measurement of aging of stem."
is_a: TO:0000361 ! stem anatomy and morphology trait
and
- stem senescence (TO:0020085) def: "A trait to measure the stem senescence."
is_a: TO:0000654 ! shoot development trait
Same problem as before:
total water soluble content
- total water soluble content (TO:0002711): def: "The concentration of water soluble components in the plant as determined by refractive index."
is_a: TO:0000281 ! metabolite content related trait
and
- total water soluble content (TO:0020088): def: "A trait to measure the concentration of water soluble components in the plant as determined by refractive index."
comment: This trait is usually highly correlated with total soluble sugar content (TO:0000340). Often determined in fresh tissue. synonym: "total dissolved solids content" EXACT [] is_a: TO:0000281 ! metabolite content related trait
- inflorescence width (TO:0000637)
- inflorescence width (TO:0000804): An inflorescence anatomy and morphology trait (TO:0000373) which is associated with the width of an inflorescence (PO:0009049).
- check definition of: TO:0020085
the term name itself should never be used (except some particular cases) to define a concept...
plant organ anatomy and morphology trait (TO:0000736) and subclasses:
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).
- 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
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.