Changes to the TO- Spring 2012

for more concise notes: Summary New TO Terms- Spring 2012

Go back to the main Plant_Trait_Ontology wiki page

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:

anatomy and morphology trait (TO:0000017)

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)

Can we just use "anatomy trait"? It would make all these names less cumbersome.

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).

need to check these now that we have changed the definition of tuber:

• 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)- needs to be updated

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

root anatomy and morphology trait (TO:0000043)

current def'n: Traits associated with changes in the anatomy or structure of the root and its parts.

propose revised def'n: root anatomy and morphology trait (TO:0000043): A plant axis anatomy and morphology trait (TO:0000738) that is associated with the root (PO:0025025).

Is a child of the new class: plant axis anatomy and morphology trait (TO:0000738)

root (PO:0025025): A plant axis that is part of a root system. [source: POC:curators]

PO Comment: Commonly thought of as one of the three basic parts of the seed plant body. A plant stucture (organ) that is usually underground and does not bear leaves and only rarely shoots, is usually more or less positively geotropic, is endogenous in origin, indeterminate in growth and often with secondary thickening.

PO hierarchy: plant organ > plant axis > shoot axis > root

PO Children of root:

• PO:0020127: primary root
• PO:0020121: lateral root
• PO:0000045: embryo root
• PO:0025002: basal root (broad: adventitious root)
• PO:0000042: shoot-borne root (broad: adventitious root)

note issue with children: adventitious root traits: in the PO adventitious root is a broad synonym of shoot-borne root and also basal root, depending where it arises from.

plant organ anatomy and morphology traits (TO:0000736)

• phyllome anatomy and morphology trait (TO:0000747)

PO hierarchy: plant organ > phyllome >leaf > vascular leaf > cotyledon

make children of new class: plant organ anatomy and morphology trait (TO:0000736): An anatomy and morphology trait (TO:0000017) which is associated with a plant organ (PO:0009008).

Add new classes:

• phyllome anatomy and morphology trait (TO:0000747): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a phyllome (PO:0006001).

• existing class: leaf anatomy and morphology trait (TO:0000419): Traits associated with changes in the anatomy or structure of the leaf and its parts.

this refers only to vascular leaves, there are 625 annotations on Gramene for this class

propose we rename to vascular leaf anatomy and morphology trait (TO:0000419). this will make it clear that it is specific to vascular leaves. See revised def'n below. This will allow all the existing children to stay on the vlamt and won't mess up the annotations as TO# will stay the same.

• new term: leaf anatomy and morphology trait (TO:0000748): A phyllome anatomy and morphology trait (TO:0000747) which is associated with a leaf (PO:0025034).

• vascular leaf anatomy and morphology trait (TO:0000419): revised def'n: A leaf anatomy and morphology trait (TO:0000748) which is associated with a vascular leaf (PO:0009025).

• cotyledon anatomy and morphology trait (TO:0000749): A vascular leaf anatomy and morphology trait (TO:0000419) which is associated with a cotyledon (PO:0020030).

completed

Requested cotyledon trait terms:

From: Syngenta (see Crop Traits Google doc)

PO term: cotyledon (PO:0020030): A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003).

• cotyledon color(TO:0000750): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the shape of a cotyledon(PO:0020030).

refer to PATO color: PATO:0000014

• cotyledon number (TO:0000751): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the number of cotyledons (PO:0020030).

refer to PATO count: PATO:0000070

• cotyledon size (TO:0000752): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the size of a cotyledon(PO:0020030).

refer to PATO size: PATO:0000117

these should all refer to the seedling cotyledon

coleoptile trait terms

PO hierarchy: plant organ > coleoptile >embryo coleoptile (PO:00252860 and seedling coleoptile (PO:0025287)

Add new terms: coleoptile anatomy and morphology trait (TO:0000753) : A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).

Move existing TO terms and refine:

• coleoptile color (TO:0000244) def: "Measure of color of the coleoptile in the germinating seedling." [GR:pj]

synonym: "COLCL" RELATED

is_a: TO:0000064 ! embryo related trait

is_a: TO:0000736 ! plant organ anatomy and morphology trait

new definition: A coleoptile anatomy and morphology trait (TO:0000753) which is associated with the color of a coleoptile (PO:0020033). refer to: color PATO:0000014

• coleoptile length (TO:0001007) def: "Measurement of the length of the coleoptile in the germinating seed." [GR:pj]

is_a: TO:0000736 ! plant organ anatomy and morphology trait

new definition:A coleoptile anatomy and morphology trait (TO:0000753) which is associated with the length of a coleoptile (PO:0020033). refer to: length PATO:0000122

Need new class: coleoptile anatomy and morphology trait (TO:0001007): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).

completed

user requested: hypocotyl color

From: Syngenta (see Crop Traits Google doc)

• seedling hypocotyl color (TO:0000759): A seedling hypocotyl anatomy and morphology trait (TO:0000769) which is associated with the color of a hypocotyl (PO:0020100). Refer to color PATO:0000014

add comment: The color of a seedling hypocotyl (PO:0025291) during the hypocotyl emergence stage (PO:0007043).

completed

color of hypocotyl at or shortly after emergence: - green, green with bronze band, purple, dark purple. PATO terms for: green, green with bronze band, purple, dark purple.

• seedling hypocotyl green (TO:0000760): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color green (PATO:0000320).

Refer to: color (PATO:0000014); green (PATO:0000320)

• seedling hypocotyl green with bronze band (TO:0000761): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color green (PATO:0000320) with a bronze (PATO:0002363) band.

• seedling hypocotyl purple (TO:0000762): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color purple (PATO:0000951).

Refer to: color (PATO:0000014); purple: PATO:0000951

• seedling hypocotyl dark purple (TO:0000763): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color dark purple (PATO:0001259).

Refer to: color (PATO:0000014); dark purple: PATO:0001259

completed

stem internode traits:

PO hierarchy: cardinal organ part > shoot internode > stem internode > hypocotyl (PO:0020100), mesocotyl (PO:0020037) and epicotyl (PO:0020035)

• shoot internode anatomy and morphology trait (TO:0000755): A cardinal organ part anatomy and morphology trait (TO:0000754) which is associated with a shoot internode (PO:0005005).

• stem internode anatomy and morphology trait (TO:0000756): A shoot internode anatomy and morphology trait (TO:0000755) which is associated with a stem internode (PO:0020142).

• hypocotyl anatomy and morphology trait (TO:0000757): A stem internode anatomy and morphology trait (TO:0000756) which is associated with a hypocotyl (PO:0020100).

• mesocotyl anatomy and morphology trait (TO:0000758): A stem internode anatomy and morphology trait (TO:0000756) which is associated with a mesocotyl (PO:0020037).

Existing TO terms: these are currently children of shoot system anatomy and morphology trait

• hypocotyl length (TO:0006065): A hypocotyl anatomy and morphology trait (TO:0000757) which is associated with the length of a hypocotyl (PO:0020100). Refer to length PATO:0000122

• mesocotyl length (TO:0000544): A mesocotyl anatomy and morphology trait (TO:0000758) which is associated with the length of a mesocotyl (PO:0020037). Refer to length PATO:0000122

completed

user requested: petiole traits

From: Syngenta (see Crop Traits Google doc)

cardinal organ part > stalk > petiole

petiole (PO:0020038): A stalk of a leaf.

Add new terms:

stalk anatomy and morphology trait (TO:0000764): A cardinal organ part anatomy and morphology trait (TO:0000754) which is associated with a stalk (PO:0025066).

petiole anatomy and morphology trait (TO:0000765): A stalk anatomy and morphology trait (TO:0000764): which is associated with a petiole (PO:0020038).

Add new terms:

petiole length (TO:0000766): A petiole anatomy and morphology trait (TO:0000765)that is associated with the length of a petiole (PO:0020038). Refer to length PATO:0000122

petiole shape(TO:0000767): A petiole anatomy and morphology trait (TO:0000765) that is associated with the shape of a petiole (PO:0020038). Refer to shape PATO:0000052

petiole size (TO:0000768): A petiole anatomy and morphology trait (TO:0000765) that is associated with the size of a petiole (PO:0020038). Refer to size PATO:0000117

completed