planteome/co_320-rice-traits

Rice trait ontology

co_320-rice-traits's Issues

Create: SPAD value

Submitter

Name	Praveen Reddy
Program	ICRISAT

Creation Request

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

method CO_320:0001274 has no method class

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	weight
Measurement Type	Unit
Measurement Unit	kg

Create: TEST: tiller number

Submitter

Name	Elizabeth Arnaud
Program	Alliance

Creation Request

Trait Name	TEST: tiller number
Definition	number of tillers
Trait Class	Agronomic
Measurement Method	counting
Measurement Type	Categorical

Categories

ID	Description
1	few (0-3)
2	medium (5-10)
3	many (>10)

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Agronomic
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	g

Create: Shoot to Root dry weight ratio

Submitter

Name	Ines Chaves
Program	IBET / ITQB NOVA

Creation Request

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

Create: leaf disease

Submitter

Name	Laurel Cooper
Program	Oregon State University

Creation Request

Trait Name	leaf disease
Definition	blah
Trait Class	Abiotic Stress
Measurement Method	color
Measurement Type	Categorical

Categories

ID	Description
1	1
****

Update: CO_320:0000146 (rice awn length trait)

Submitter

Name	Laurel Cooper
Program	Planteome

Update Request

Term	CO_320:0000146 (rice awn length trait)
Description of Change	Testing functionality
Rational	Could use a more descriptive definition.

Create: Shoot to Root dry weight ratio

Submitter

Name	Ines Chaves
Program	IBET / ITQB NOVA

Creation Request

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

Create: test trait

Submitter

Name	Laurel Cooper
Program	Dept. of Botany and Plant Pathology, Oregon State University

Creation Request

Trait Name	test trait
Proposed Synonyms	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	test
Measurement Type	Unit
Measurement Unit	kg

Update: CO_320:0000030 (rice culm length trait)

Submitter

Name	Laurel
Program	Planteome
Email	[email protected]

Update Request

Term	CO_320:0000030 (rice culm length trait)
Description of Change	test
Rational	test

Create: test 345

Submitter

Name	Justin Elser
Program	OSU

Creation Request

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

Update: CO_320:0000030 (rice culm length trait)

Submitter

Name	Laurel
Program	Planteome
Email	[email protected]

Update Request

Term	CO_320:0000030 (rice culm length trait)
Description of Change	test
Rational	test

Suggest rename "rice grain discoloration trait" (CO_320:0000499)

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"

Create: plant height

Submitter

Name	Liliana Andres Hernandez
Program	SCU

Creation Request

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

Create: test56235

Submitter

Name	Krishna Udaiwal
Program	NA

Creation Request

Trait Name	test56235
Proposed Synonyms	test53124
Definition	test3215151
Trait Class	Quality
Measurement Method	visual
Measurement Type	Unit
Measurement Unit	cnt

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	g

Missing scale and/or method for 3 traits

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

Create: Test Rice Trait Name

Submitter

Name	Abenet
Program	ILRI

Creation Request

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

Missing traits

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

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	weight
Measurement Type	Unit
Measurement Unit	kg

Create: test

Submitter

Name	Krishna Udaiwal
Program	NA

Creation Request

Trait Name	test
Proposed Synonyms	test2
Definition	test test
Trait Class	Quality
Measurement Method	visual
Measurement Type	Categorical

Categories

ID	Description
1	test3
2	test4

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	g

Create: test45

Submitter

Name	Krishna Udaiwal
Program	NA

Creation Request

Trait Name	test45
Proposed Synonyms	test54
Definition	test test
Trait Class	Quality
Measurement Method	visual
Measurement Type	Unit
Measurement Unit	count

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Biotic Stress
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	cg

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	cgs

Update: CO_320:0000146 (rice awn length trait)

Submitter

Name	Laurel Cooper
Program	Planteome

Update Request

Term	CO_320:0000146 (rice awn length trait)
Description of Change	Testing
Rational	Could use a more descriptive definition

Categorical classes are still present in rice CO

Create: test

Submitter

Name	Justin Elser
Program	OSu

Creation Request

Trait Name	test
Definition	test
Trait Class	Abiotic Stress
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	g

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

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

rice seeding date CO_320:0000514

This is not a trait
https://browser.planteome.org/amigo/term/CO_320:0000514

Variable request form is giving an error on "Update variable"

http://trait-requests.planteome.org/

After submission- "Internal Server Error"

TD5 TSV file must be included (not csv)

See: Planteome/plant-trait-ontology#374

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Agronomic
Measurement Method	rate
Measurement Type	Unit
Measurement Unit	g

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Morphological
Measurement Method	weight
Measurement Type	Unit
Measurement Unit	kg

obo file is invalid

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.

Create: Test tiller number

Submitter

Name	Marie-Angélique Laporte
Program	Alliance of Bioversity International and CIAT

Creation Request

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

Categories

ID	Description
1	few
2	lot

Create: test

Submitter

Name	Krishna Udaiwal
Program	NA

Creation Request

Trait Name	test
Proposed Synonyms	test2
Definition	test test
Trait Class	Quality
Measurement Method	test
Measurement Type	Categorical

Categories

ID	Description
1	catastrophic
2	minor

Create: test

Submitter

Name	Justin Elser
Program	OSU

Creation Request

Trait Name	test
Definition	test
Trait Class	Agronomic
Measurement Method	v
Measurement Type	Unit
Measurement Unit	g