planteome / co_320-rice-traits Goto Github PK
View Code? Open in Web Editor NEWRice trait ontology
Home Page: https://cropontology.org/term/CO_320:ROOT
Rice trait ontology
Home Page: https://cropontology.org/term/CO_320:ROOT
Name | Liliana Andres Hernandez |
Program | SCU |
Trait Name | plant height |
Definition | The measurement of plant from top to bottom |
Trait Class | Morphological |
Measurement Method | Measurement |
Measurement Type | Unit |
Measurement Unit | cm |
Name | Laurel Cooper |
Program | Planteome |
Term | CO_320:0000146 (rice awn length trait) |
Description of Change | Testing |
Rational | Could use a more descriptive definition |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | weight |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Morphological |
Measurement Method | weight |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Krishna Udaiwal |
Program | NA |
Trait Name | test |
Proposed Synonyms | test2 |
Definition | test test |
Trait Class | Quality |
Measurement Method | test |
Measurement Type | Categorical |
ID | Description |
---|---|
1 | catastrophic |
2 | minor |
Name | Laurel Cooper |
Program | Dept. of Botany and Plant Pathology, Oregon State University |
Trait Name | test trait |
Proposed Synonyms | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | test |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Justin Elser |
Program | OSu |
Trait Name | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | g |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | cgs |
Name | Laurel Cooper |
Program | Planteome |
Term | CO_320:0000146 (rice awn length trait) |
Description of Change | Testing functionality |
Rational | Could use a more descriptive definition. |
This is not a trait
https://browser.planteome.org/amigo/term/CO_320:0000514
Name | Praveen Reddy |
Program | ICRISAT |
Trait Name | SPAD value |
Definition | Chlorophyll measurement on the flag leaf at flowering |
Trait Class | Morphological |
Measurement Method | SPAD value at booting |
Measurement Type | Unit |
Measurement Unit |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | This is a test to check the new github authorization |
Trait Class | Abiotic Stress |
Measurement Method | visual |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Agronomic |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | g |
Name | Justin Elser |
Program | OSU |
Trait Name | test 345 |
Proposed Synonyms | test 456 |
Definition | test trait |
Trait Class | Abiotic Stress |
Measurement Method | visual rating |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Abenet |
Program | ILRI |
Trait Name | Test Rice Trait Name |
Definition | This is a test rice trait name definition |
Trait Class | Abiotic Stress |
Measurement Method | This is a test of the method of mesaurement |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Krishna Udaiwal |
Program | NA |
Trait Name | test45 |
Proposed Synonyms | test54 |
Definition | test test |
Trait Class | Quality |
Measurement Method | visual |
Measurement Type | Unit |
Measurement Unit | count |
Name | Ines Chaves |
Program | IBET / ITQB NOVA |
Trait Name | Shoot to Root dry weight ratio |
Proposed Synonyms | Shoot to Root dry weight ratio |
Definition | Shoot to Root dry weight ratio |
Trait Class | Physiological |
Measurement Method | "Computational:Shoot to Root dry weight ratio:Shoot DW divided by root DW. DW was determined after drying plant material at 70ºC (until a constant weight was achieved) S:R = SDW/RDW" |
Measurement Type | Unit |
Measurement Unit | units |
Name | Krishna Udaiwal |
Program | NA |
Trait Name | test |
Proposed Synonyms | test2 |
Definition | test test |
Trait Class | Quality |
Measurement Method | visual |
Measurement Type | Categorical |
ID | Description |
---|---|
1 | test3 |
2 | test4 |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | g |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Agronomic |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | g |
I suggest renaming "rice grain discoloration trait" (CO_320:0000499) to "rice glumes discoloration trait" (CO_320:0000499), to better reflect the meaning of the definition:
"The extent of discoloration of glumes caused by species of Sarocladium, Bipolaris, Alternaria, Gerlachia, Fusarium, Phoma, Curcularia, Trichoconiella, and Pseudomonas. Symptoms: Darkening of glumes of spikelets, brown color to black including rotten glumes. Intensity ranges from sporadic discoloration to discoloration of the whole glume"
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | weight |
Measurement Type | Unit |
Measurement Unit | kg |
Name | Marie-Angélique Laporte |
Program | Alliance of Bioversity International and CIAT |
Trait Name | Test tiller number |
Definition | number of tillers |
Trait Class | Morphological |
Measurement Method | count the number of tiller using a computer |
Measurement Type | Categorical |
ID | Description |
---|---|
1 | few |
2 | lot |
Name | Krishna Udaiwal |
Program | NA |
Trait Name | test56235 |
Proposed Synonyms | test53124 |
Definition | test3215151 |
Trait Class | Quality |
Measurement Method | visual |
Measurement Type | Unit |
Measurement Unit | cnt |
http://trait-requests.planteome.org/
After submission- "Internal Server Error"
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Biotic Stress |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | cg |
Name | Ines Chaves |
Program | IBET / ITQB NOVA |
Trait Name | Shoot to Root dry weight ratio |
Proposed Synonyms | Shoot to Root dry weight ratio |
Definition | Shoot to Root dry weight ratio |
Trait Class | Physiological |
Measurement Method | Computational:Shoot to Root dry weight ratio:Shoot DW divided by root DW. DW was determined after drying plant material at 70ºC (until a constant weight was achieved) S:R = SDW/RDW |
Measurement Type | Unit |
Measurement Unit |
Name | Laurel |
Program | Planteome |
[email protected] |
Term | CO_320:0000030 (rice culm length trait) |
Description of Change | test |
Rational | test |
Name | Laurel Cooper |
Program | Oregon State University |
Trait Name | leaf disease |
Definition | blah |
Trait Class | Abiotic Stress |
Measurement Method | color |
Measurement Type | Categorical |
ID | Description |
---|---|
1 | 1 |
**** |
Name | Laurel |
Program | Planteome |
[email protected] |
Term | CO_320:0000030 (rice culm length trait) |
Description of Change | test |
Rational | test |
Name | Elizabeth Arnaud |
Program | Alliance |
Trait Name | TEST: tiller number |
Definition | number of tillers |
Trait Class | Agronomic |
Measurement Method | counting |
Measurement Type | Categorical |
ID | Description |
---|---|
1 | few (0-3) |
2 | medium (5-10) |
3 | many (>10) |
Hello,
I've been annotating a rice dataset from this article and I noticed that some traits were missing.
I would like to suggest the inclusion of these following traits, with respective method and scale
missing_variables_rice_CO320.xlsx that are missing in the Rice ontology.
[root|shoot] [dry|fresh] weight
Clorophyll [a|b] content
Na+|K+ [Shoot|Root] content
and Leaf osmotic Potential
Hi,
I work as data manager at URGI (INRA of Versailles, France). I would like to submit 3 new variables to Crop Ontology (here : missing variables Melanie Buy.xlsx), after working on some datasets for CIRAD (Montpellier, France). I have already sent these variables to Elizabeth Arnaud, and she told me it could be convenient to open an issue too.
Thank you,
Mélanie Buy
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Agronomic |
Measurement Method | v |
Measurement Type | Unit |
Measurement Unit | g |
Name | Justin Elser |
Program | OSU |
Trait Name | test |
Definition | test |
Trait Class | Abiotic Stress |
Measurement Method | rate |
Measurement Type | Unit |
Measurement Unit | g |
For context to this ticket, see checklist: Planteome/plant-trait-ontology#374
This line is invalid:
https://github.com/Planteome/ibp-rice-traits/blob/master/rice-trait-ontology.obo#L54
last line in the stanza:
[Term]
id: CO_320:0000005
name: grain width
def: "Width of the dehulled grain with pericarp." [CO:rs]
comment: Enter the actual measurement of width in millimeters as the distance across the fertile lemma and the palea at the widest point.
synonym: "GrW" EXACT []
synonym: "seed width" RELATED []
xref: IRIS_TRAITID:1052
xref: TO:0000149
xref: TO:0000402
is_a: CO_320:0000001 ! morphological trait
Sample size = 10. At growth stage: 9.
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