Changes to the TO- Spring 2012
Summary New TO Terms- Spring 2012
Changes to root term:
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
Changes to top level classes:
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)
New children of anatomy and morphology 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).
