Trait Ontology Submission

[planteome-user]

A record of our submission on 2008-01-09

Reported by: dsenalik

Original Ticket: "obo/plant-trait-ontology-to-requests/23":https://sourceforge.net/p/obo/plant-trait-ontology-to-requests/23

[planteome-user]

The original submission log lacked all of the "parent term" text, perhaps a bug in the web form? Anyway, I put those back in, fixed a few blank boxes, and cleaned up the formatting. And added one more term. File Added: TOSubmissions for SourceForge version-modified.xls

Original comment by: dsenalik

[planteome-user]

Request: TO:0000496 carotenoid content is a subset of flavonoid content (TO:0000290), which is wrong, it should be instead a subset of phytochemical compound content (TO:0000674)

pj: accepted. Fixed.

request: root cracking: Physical cracking of a storage root caused by genetic or environmental factors, or by post-harvest handling

pj: Suggested definition: Physical cracking of a root caused by genetic or environmental factors, or by post-harvest storage and handling of the root part.

request: seed spines: The number, size, or physical distribution of spines on the seed pj: -Which species are we looking at. -Are these the same as 'seed trichomes/hairs' -number/size/distribution are actually three different traits.

We have something similar 'leaf pubescence': Extent of presence (presence of hairs) on the leaf blade surface. If you are looking at the similar structures we can create terms like 'seed pubescence'

request: total dissolved solids content: The concentration of water soluble components in the plant as determined by refractive index. This trait is usually highly correlated with total soluble sugar content (TO:0000340)

pj: -can we call it 'total water soluble content'. -are you looking at fresh/dried tissue sample/whole plant.

Following terms were added. Working on others on bulb and cloves.

[Term] id: TO:0002694 name: flavor trait def: "An assay to detrmine the sensory impression of a food product or other substance by the chemical senses of taste and smell." [GR:pj] is_a: TO:0000281 ! metabolite content related trait is_a: TO:0000597 ! quality trait

[Term] id: TO:0002695 name: beta-carotene content def: "The beta-carotene content in a plant or plant part. " [GR:pj] comment: beta-carotene is the most common form of carotenoid. exact_synonym: "beta-carotenoid content" [] is_a: TO:0002697 ! cyclic carotene content

[Term] id: TO:0002696 name: alpha carotene content def: "The alpha-carotene content in a plant or plant part. " [GR:pj] comment: alpha-carotene is the second most common form of carotenoid. exact_synonym: "alpha-carotenoid content" [ ] is_a: TO:0002697 ! cyclic carotene content

[Term] id: TO:0002697 name: cyclic carotene content def: "The cyclic carotene content in a plant or plant part. " [GR:pj] is_a: TO:0000289 ! carotene content

[Term] id: TO:0002698 name: acyclic carotene content def: "The acyclic carotene content in a plant or plant part. " [GR:pj] is_a: TO:0000289 ! carotene content

[Term] id: TO:0002699 name: lycopene content def: "The lycopene content in a plant or plant part. " [GR:pj] comment: Lycopene is the most efficient quencher of singlet oxygen free radicals. is_a: TO:0002698 ! acyclic carotene content

[Term] id: TO:0002700 name: pungency def: "The quality of producing a sharp sensation of taste or smell." [GR:pj] is_a: TO:0002694 ! flavor trait

[Term] id: TO:0002701 name: lutein content def: "The leutein content in a plant or plant part. " [GR:pj] is_a: TO:0000301 ! xanthophyll content

[Term] id: TO:0002702 name: cercospora leaf spot resistance def: "Causal agent: Cercospora spp." [GR:pj] is_a: TO:0000439 ! fungal disease resistance

[Term] id: TO:0002703 name: protist disease resistance def: "The resistance exhibited by a plant or a group of plants (population) in response to the disease caused by a protist infection as compared to the susceptible and/or the reference plants of the same species." [GR:pj] is_a: TO:0000112 ! disease resistance

[Term] id: TO:0002704 name: Meloidogyne incognita resistance def: "Causal agent: Meloidogyne incognita. Symptom: resistant to damage caused by the pathogen Meloidogyne incognita (root knot nematode). It produces characteristic galls (swellings) on roots." [GR:pj] is_a: TO:0000384 ! nematode damage resistance

[Term] id: TO:0002705 name: cucurbit downy mildew resistance def: "Causal agent: Pseudoperonospora cubensis. It causes the downy mildew disease in cucurbits." [GR:pj] is_a: TO:0000439 ! fungal disease resistance

[Term] id: TO:0002706 name: Meloidogyne javanica resistance def: "Causal agent: Meloidogyne javanica. Symptom: resistant to damage caused by the pathogen Meloidogyne javanica (root knot nematode). It produces characteristic galls (swellings) on roots." [GR:pj] is_a: TO:0000384 ! nematode damage resistance

[Term] id: TO:0002707 name: petiole color def: "The color of the petiole." [GR:pj] relationship: part_of TO:0000326 ! leaf color

[Term] id: TO:0002708 name: xylem color def: "The color of the xylem tissue." [GR:pj] is_a: TO:0000470 ! vascular tissue related trait

[Term] id: TO:0002709 name: phloem color def: "The color of the phloem tissue." [GR:pj] is_a: TO:0000470 ! vascular tissue related trait

[Term] id: TO:0002710 name: root shape def: "The shape of the plant root system." [GR:pj] is_a: TO:0000043 ! root anatomy and morphology trait

[Term] id: TO:0002711 name: total water soluble content def: "The concentration of water soluble components in the plant as determined by refractive index. " [GR:pj] is_a: TO:0000281 ! metabolite content related trait

Original comment by: jaiswalp

[planteome-user]

request: root cracking: Physical cracking of a storage root caused by genetic or environmental factors, or by post-harvest handling

pj: Suggested definition: Physical cracking of a root caused by genetic or environmental factors, or by post-harvest storage and handling of the root part.

ds: Ok, this is fine.

request:

• total dissolved solids content: The concentration of water soluble components in the plant as determined by refractive index. This trait is usually highly correlated with total soluble sugar content (TO:0000340)

pj: -can we call it 'total water soluble content'. -are you looking at fresh/dried tissue sample/whole plant.

ds: This is always in fresh tissue, in our case in carrot roots, but it is used for many crops, e.g. tomato fruits 'total water soluble content' is fine, but maybe we can add a note in the comment such as " this is commonly also referred to as total dissolved solids"

request: seed spines: request: bulb / clove/ etc. we are discussing these two, and will let you know later

[planteome-user]

[Term] id: TO:0020087 name: root cracking def: "A trait measuring the extent of physical cracking of a root caused by genetic, environmental factors or by post-harvest storage and handling of the root or root part." [GR:pj] is_a: TO:0000168 ! abiotic stress trait created_by: jaiswalp creation_date: 2011-08-19T03:44:21Z

[Term] id: TO:0020088 name: total water soluble content 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 created_by: jaiswalp creation_date: 2011-08-19T03:47:00Z

Original comment by: jaiswalp