Difference between revisions of "Plant Trait Ontology"
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''Not sure where to put these right now- TBA'' | ''Not sure where to put these right now- TBA'' | ||
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===plant cell anatomy and morphology trait=== | ===plant cell anatomy and morphology trait=== | ||
Revision as of 15:23, 21 April 2012
This page will be a place to keep track of the work on developing the Plant Trait Ontology
New:
Call for papers: Knowledge Engineering and Ontology Development
Crop Plant Trait Ontology paper
Also: Ontologies and semantic technologies for agricultural knowledge in practice
Related Wiki Pages and Links:
Details about the plans for the Crop_Ontology_Workshop_at_OSU,_2012
Work on the wood traits: Goal_3._Wood_qualities_and_phenotypes
TO Tracker on SourceForge
Trait Ontology on Bioportal: TO
Links to Collaborator Sites:
GCP Phenotype and Trait Ontology
Look into Grin Global- Peter Bretting, David Okomuri
Trait lists on Google docs
Triticeae Toolbox Traits for Wheat
Ontology Issues:
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.
background on the GO classes:
- 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.
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.
Includes all the enzyme activities such as catalysis of a biochemical reaction, regulation, binding, nucleic acid binding (transcription factor), receptor activity, transporter activity,etc
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.
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).
note: The PO ids in the comments do not go into the Dbxrefs
may move this stuff to this page: 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).
- 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).
- 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).
- 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).
tuber traits
Terms requested by Syngenta (in bold):
tuber (PO:0004543): An enlarged storage branch (PO:0025073)
probably should be: subterranean tuber (PO:0004547): A tuber (PO:0004543) that is below ground
tuber epidermis (PO:0025046): A portion of shoot axis epidermis that is part of a tuber (PO:0004543).
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
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).
broad synonym:tuber eye
tuber storage parenchyma (PO:0025036): A portion of storage parenchyma (PO:0025035) that is part of a tuber (PO:0004543). exact synonym:tuber flesh
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).
Narrow Synonym: potato tuber flesh
need to update in PO
requested terms and suggested def'ns:
tuber shape- The shape of the tuber
tuber size- The physical size of the tuber
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)
tuber mass- The mass of the tuber
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
- tuber shape
Proposed new term and def'n: 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
refer to PATO shape: PATO:0000052
- tuber size
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
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
shoot anatomy and morphology trait (TO:0000077)
current def'n: 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.
propose 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).
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.
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.
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
- coleoptile color (plant organ)
- 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
- relative shoot elongation under submergence (plant organ > plant axis > shoot axis (syn: shoot))
- 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
- 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
plant cell anatomy and morphology trait
- plant cell length
- plant cell shape
- plant cell size
cell organelle structure trait
- plastid development trait
fruit structure trait
- fruit abscission zone size
- fruit shape
- fruit size
seed anatomy and morphology trait
- embryo related trait
- endosperm related trait
- seed coat color
- seed color
- seed shape
- seed texture
Also:
- root anatomy and morphology trait
- vascular tissue related trait
- plant aspect (should go under whole plant)
whole plant trait TO:0000398
has been obsoleted, maybe we should consider bringing back?
