Difference between revisions of "Plant Trait Ontology"
| Line 63: | Line 63: | ||
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. | 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 changes in the anatomy or structure of a plant anatomical entity (PO:0000003) or a cellular component that is part of, or has participant a plant anatomical entity (PO:0000003). | + | proposed def'n: A plant trait (TO:0000387) which is associated changes in the anatomy or structure of a plant anatomical entity (PO:0000003) or a cellular component (GO:0005575) that is part of, or has participant a plant anatomical entity (PO:0000003). |
Children: | Children: | ||
Revision as of 19:29, 18 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
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.
- 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 changes in the anatomy or structure of a plant anatomical entity (PO:0000003) or a cellular component (GO:0005575) that is part of, or has participant a plant anatomical entity (PO:0000003).
Children: cell organelle structure trait
- fruit structure trait
- plant aspect
- plant cell anatomy and morphology trait
- root anatomy and morphology trait
- seed anatomy and morphology trait
- shoot anatomy and morphology trait
- vascular tissue related trait
problem with this currently is that it does not include whole plant traits, but has children such as plant height (is_a shoot anatomy and morphology trait)
whole plant trait
has been obsoleted, maybe we should consider bringing back?
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.
proposed def'n:
tuber traits:
tuber (PO:0004543): An enlarged storage branch
subterranean tuber (PO:0004547): A tuber that is below ground
tuber epidermis (PO:0025048): subterranean tuber epidermis
tuber flesh (PO:0025038): subterranean tuber storage parenchyma
tuber eye (PO:0025042): subterranean tuber axillary vegetative bud
requested terms:
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
