planteome/co_334-cassava-traits

Cassava Trait Ontology maintained by Crop Ontology and Cassavabase

co_334-cassava-traits's Issues

plant height measurement in cm at 6 months after planting

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	plant height measurement in cm at 6 months after planting
Definition	Vertical height of plants from the ground to top of the canopy measured in centimeter (cm), 6 months after planting.

 |

| Trait Class | Morphological |
| Measurement Method | measured with ruler |
| Measurement Type | Unit |
| Measurement Unit | cm |

Typos in NIRS-related terms

General comments:

• NIRS = near-infrared spectroscopy, not Near InfraRed Spectrophotometry
• wavelength ranges should be specified with units (nm for all of the terms below)
• the plural of "spectrum" is "spectra"

Specific changes:

CO_334:0002056

• name should be: dry matter content by SCiO in percentage (C is capitalized in SCiO)
• def should be: "Percentage dry matter content estimated using the SCiO, a miniature handheld near-infrared (NIR) spectrometer. Output are spectra with a range of 740 to 1070nm and are converted to percentage using a prediction model."

CO_334:0010508

• name should be: Dry matter content by SCiO_method (again, just capitalize the C)
• def should be: "Prediction of dry matter content using spectra generated by the SCiO, a miniature handheld NIRS device (740-1070nm) done by placing the device consistently on three different parts of dissected root sections (proximal, axial and distal)."

CO_334:0002057 and CO_334:0010509

• these terms need to be more specific, as there are many different tabletop NIR spectrometers, not all with the wavelength range described in the def here. Each needs its own term to be consistent with the terms for the QST and SCiO and to allow for compatibility with analysis tools

CO_334:0002058

• def should be: "Percentage dry matter content estimated using the QualitySpec Trek, a handheld near-infrared (NIR) spectrometer. Output are spectra with wavelength range of 350-2500nm, and are converted percentage by a prediction model."

CO_334:0010507

• def should be: "Prediction of dry matter content using spectra generated by handheld NIRS device (wavelength range of 350-2500nm) done by placing the device consistently on three different parts of dissected root sections (proximal, axial and distal)."

Odd Xrefs on CO_334:0000015 cassava harvest index variable

The xrefs in the stanza below are incorrect or in the incorrect place, as they show up on the browser in the mappings field. See: http://dev.planteome.org/amigo/term/CO_334:0000015
This xref:' ICASS_TRAITID:10045' should probably be in the definition xrefs, and this one: 'xref: TO:0000128 "Plant trait ontology" ' should be removed, as we don't have the mappings to TO on the variable terms.

Also TO:0000128 is 'harvest index'

[Term]
id: CO_334:0000015
name: cassava harvest index variable
def: "Proportion of fresh root weight in total biomass." [CO:curators]
synonym: "HI" EXACT []
xref: ICASS_TRAITID:10045
xref: TO:0000128 "Plant trait ontology"
relationship: derives_from CO_334:0000013 ! fresh root yield
relationship: derives_from CO_334:0000017 ! top yield
relationship: variable_of CO_334:0000267 ! Harvest index

Create: Pasting temperature

Submitter

Name	Michael Kanaabi
Program	NaCRRI

Creation Request

Trait Name	Pasting temperature
Definition	Temperature at which the viscosity trace first raises above the baseline during the initial heating phase.
Trait Class	Quality
Measurement Method	Measured by the Rapid Visco Analyser (RVA)
Measurement Type	Unit
Measurement Unit	Degrees Celsius

uniformization dry matter content traits and variables

2 traits exist and are related to dry matter content.

[Term]
id: CO_334:0000424
name: Root dry matter content
namespace: cassava_trait
def: "Dry matter content of root related terms." [CO:curator]
is_a: CO_334:0000447 ! Dry matter content
created_by: AAfolabi
creation_date: 2017-07-18T14:58:31Z

When looking at the variables, some refer to this Root dry matter content but some refer to its parent term, Dry matter content, even if they seem to be root variables.

Actions:

• create more subclasses for the term Dry matter content as needed (e.g. a Leaf dry matter content)
• map the variables to the more specific term (Root DMC, Leaf DMC, ...)

Variables linked to the parent Dry matter content:

• CO_334:0000163 - specific gravity
• CO_334:0000385 - dry matter content of lower stem percentage
• CO_334:0000423 - dry matter content of leaf percentage
• CO_334:0002012 - dry matter visual rating 1-3

inconsistencies between obo file and TD - CO_334:0000077

The scale information is missing in the obo file for this variable yet it is described in the TD as:

CO_334:0100678	11pt scale	Ordinal					0 = No symptom of root discoloration	3 = 30% of the root surface has root discoloration	4 = 40% of the root surface has root discoloration	1=10% of the root surface has root discoloration	2 = 20% of the root surface has root discoloration	7 = 70% of the root surface has root discoloration	8 = 80% of the root surface has root discoloration	5 = 50% of the root surface has root discoloration	6 = 60% of the root surface has root discoloration	10 = 100% of the root surface has root discoloration

Since the ID CO_334:0100678 is used in the obo file, I would recommend to add back this scale with a different ID.

Variable info in the obo file:

[Term]
id: CO_334:0000077
name: cassava post-harvest physiological deterioration variable 0-10 variable
def: "Internal root discoloration or vascular streaking that renders cassava roots unfit for human or animal consumption.\nA number of root samples are cut into 7 slices  and each slice is scored on a 0-10 scale." [CO:curators]
relationship: variable_of CO_334:0000266 ! post-harvest physiological deterioration
relationship: variable_of CO_334:0010001 ! Estimation: post-harvest physiological deterioration method

Add farmer trait preferences at harvest and post harvest

Farmers were given three(3) varieties each and they give their opinion on each, rank and and as well score on an ordinal scale of 1-5.

More tests, sorry!

Submitter

Name	Test of moved template
Program	blah blah

Request

Trait Name	More tests, sorry!
Definition	test
Trait Class	Abiotic Stress
Measurement Method	twst
Measurement Type	Unit
Measurement Unit	test

Create: Peak

Submitter

Name	Michael Kanaabi
Program	NaCRRI

Creation Request

Trait Name	Peak
Proposed Synonyms	Peak viscosity, Maximum hot paste viscosity
Definition	Maximum viscosity during the heating or hold phase of the RVA test
Trait Class	Quality
Measurement Method	Measured by the Rapid Visco Analyser (RVA)
Measurement Type	Unit
Measurement Unit	Degrees Celsius

Number of inflorescence by branch level

Number of inflorescence by branch level should not be a subclass of days to first inflorescence. It should go under CO_334:0000336 ! Flower and flowering morphological trait

[Term]
id: CO_334:0000525
name: Number of inflorescence by branch level
namespace: cassava_trait
def: "Number of inflorescence at specific branching level." [CO:curator]
is_a: CO_334:0000359 ! Days to first inflorescence
created_by: AAfolabi
creation_date: 2017-07-25T15:54:07Z

Create: Canopy lenght measured in centimeters

Submitter

Name	LUCIANO ROGERIO BRAATZ DE ANDRADE
Program	EMBRAPA

Creation Request

Trait Name	Canopy lenght measured in centimeters
Definition	Canopy length evaluation
Trait Class	Morphological
Measurement Method	length measurement with metric ruler for centimeter
Measurement Type	Unit
Measurement Unit	cm

Beta Carotene in dry matter

Submitter

Name	Edda Mushi
Program	IITA

Request

Trait Name	Beta Carotene in dry matter
Definition	Beta Carotene measurement
Trait Class	Quality
Measurement Method	Beta Carotene measured with HPLC at harvest stage on the root using 3 samples
Measurement Type	Categorical

Categories

ID	Description
1	low
2	medium
3	high

Create: Canopy width measured in centimeters

Submitter

Name	LUCIANO ROGERIO BRAATZ DE ANDRADE
Program	EMBRAPA

Creation Request

Trait Name	Canopy width measured in centimeters
Definition	length measurement with metric ruler in centimeter
Trait Class	Morphological
Measurement Method	width measurement with metric ruler in centimeters
Measurement Type	Unit
Measurement Unit	cm

Create: Texture Max Force

Submitter

Name	Karima Meghar
Program	Cirad

Creation Request

Trait Name	Texture Max Force
Proposed Synonyms	TMF
Definition	Texture of boiled cassava
Trait Class	Quality
Measurement Method	Texture measurement
Measurement Type	Unit
Measurement Unit	g

change TO mapping to xrefs?

can we update the TO mappings from is_a relationship to xrefs?
e.g.
https://github.com/Planteome/ibp-cassava-traits/blob/master/cassava-trait-ontology.obo#L84

Create: root weight 6 months

Submitter

Name	gbauchet
Program	BTI
Email	[email protected]

Creation Request

Trait Name	root weight 6 months
Proposed Synonyms	RW6Mth
Definition	root weight for 10 plants per plot at 6 month after planting
Trait Class	Agronomic
Measurement Method	Measure on a scale
Measurement Type	Unit
Measurement Unit	kg

Storage root weight by plot

Storage root weight by plot - CO_334:0000302 - has not definition and is defined in the obo file as being a storage root weight - CO_334:0000493

2 solutions:

• add a definition to the trait
• replace CO_334:0000302 by CO_334:0000493 in the obo file (in the TD, only CO_334:0000493 is used).

Which of these 2 solutions should be implemented ? @aafolabi @nmenda

Make cassava ontology variable names unique

Variable names should be different from the trait names.
Fola is working on updating variables from the 'Agronomic trait' node.

Will then test this on cassavabase before updating the rest of the terms.

typo in the name of trait CO_334:0000470

Should be 'days to abortion'

Cassava file for loading on AmiGO browser should not be in a separate branch

It would be better to keep the files together in the master branch. We can differentiate them by the names.

add method and scale for variable CO_334:0002050

CO_334:0002050 'cooking quality visual rating 0-2' is only linked to a trait

plant height measurement in cm at 3 months after planting

Submitter

Name	luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	plant height measurement in cm at 3 months after planting
Definition	Vertical height of plants from the ground to top of the canopy measured in centimeter (cm), 3 months after planting.
Trait Class	Morphological
Measurement Method	measured with ruler
Measurement Type	Unit
Measurement Unit	cm

plant height measurement in cm at 9 months after planting

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	plant height measurement in cm at 9 months after planting
Definition	Vertical height of plants from the ground to top of the canopy measured in centimeter (cm), 9 months after planting.
Trait Class	Morphological
Measurement Method	measured with ruler
Measurement Type	Unit
Measurement Unit	cm

Create: dry weight above ground plant

Submitter

Name	Peter Hyde
Program	cornell university
Email	[email protected]

Creation Request

Trait Name	dry weight above ground plant
Proposed Synonyms	DwAbGrd
Definition	total plant mass above ground (stem+ leaves + petiole)
Trait Class	Agronomic
Measurement Method	dried in oven for 10 days at 50 degree celsius and weighted using scale
Measurement Type	Unit
Measurement Unit	kg

Rust disease incidence

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	Rust disease incidence 6-month evaluation
Definition	Proportion of plants within a plot showing symptoms of Rust, evaluated close to six months after planting.
Trait Class
Measurement Method	Proportion of plants within a plot showing symptoms of Rust
Measurement Type	Unit
Measurement Unit	%

Add "automated whitefly count" and "automated necrosis detection" methods to the relevant whitefly and necrosis traits

Create: Trough

Submitter

Name	Michael Kanaabi
Program	NaCRRI

Creation Request

Trait Name	Trough
Proposed Synonyms	Trough viscosity, Hold, Holding strength, Holding viscosity
Definition	The minimum viscosity after the peak
Trait Class	Quality
Measurement Method	Measured with the Rapid Visco Analyzer (RVA)
Measurement Type	Unit
Measurement Unit	pascal second (Pa-s)

Add other term series for post composed trait

Add term series for phenotyping done in tiers.

Root section

• Proximal
• Axial
• Distal

Stem portion

• Hardwood (lower woody stem portion)
• Semi-hardwood (mid part)
• Green shoot
• Tip shoot

Leaf area
Leaves can be collected from different parts of the stem

• Hardwood (lower woody stem portion)
• Semi-hardwood (mid part)
• Green shoot
• Tip shoot

Treatment type

• Raw
• Boiled
• Fried
• Dried

Rust disease incidence 9-month evaluation

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	Rust disease incidence 9-month evaluation
Definition	Proportion of plants within a plot showing symptoms of Rust, evaluated close to nine months after planting.

 |

| Trait Class | Biotic Stress |
| Measurement Method | Proportion of plants within a plot showing symptoms of Rust |
| Measurement Type | Unit |
| Measurement Unit | % |

Add mappings to TO

See checklist: Planteome/plant-trait-ontology#374

Currently there are neither xrefs in the .obo nor a column in the TD5 xls

Add missing variables from Cassavabase

77, 123, 224, and 256 are missing from the CO file
e.g.
http://www.cassavabase.org/chado/cvterm?action=view&cvterm_id=76806

shoot apex compactness

The trait shoot apex compactness used to have the ID CO_334:0000272, which is now assigned to the variable female flower number counting on all levels.

CO_334:0000272	Shoot apex compactness	Agronomical trait	Compactness of the shoot apex		ShApCmp		Shoot apex	Compactness	Recommended

Since the variable CO_334:0000270 (compactness of shoot apices visual 1-3) is really about the compactness of the apices, I would recommend to recreate the trait Shoot apex compactness as it was using a different ID and using it to define the variable CO_334:0000270.

cassava test

Submitter

Name	Laurel Cooper
Program	cassava

Request

Trait Name	cassava test
Definition	testing.....
Trait Class	Morphological
Measurement Method	visual assesment
Measurement Type	Categorical

Categories

ID	Description
1	test
2	test

Create: Final viscosity

Submitter

Name	Michael Kanaabi
Program	NaCRRI

Creation Request

Trait Name	Final viscosity
Proposed Synonyms	End viscosity
Definition	Viscosity at the end of the RVA test
Trait Class	Quality
Measurement Method	Measured using the Rapid Visco Analyzer (RVA)
Measurement Type	Unit
Measurement Unit	Pascal_second (Pa-s)

first apical branch height measurement in cm, at 6 months after planting

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	first apical branch height measurement in cm, at 6 months after planting
Definition	Height of first apical branch (ground level to point of first Apical branch, 6 months after planting) in cm.

 |

| Trait Class | Morphological |
| Measurement Method | measured with Ruler |
| Measurement Type | Unit |
| Measurement Unit | cm |

Question about cassava disc color trait (CO_334:0000360)

Is this the color of the flowers or a disc of the tuber? I am not sure where to map it to without knowing that. The term TO:1000019 ! disk flower color refers to disk flowers in a capitulum type inflorescence, such as those in the Asteraceae, which is different than those in Cassava.
http://dev.planteome.org/amigo/term/PO:0025332

[Term]
id: CO_334:0000360
name: cassava disc color trait
def: "Color of disc" [CO:curators]
synonym: "discol" EXACT []
is_a: TO:1000019 ! disk flower color

Create: Breakdown

Submitter

Name	Michael Kanaabi
Program	NaCRRI

Creation Request

Trait Name	Breakdown
Definition	Breakdown equals peak viscosity minus trough viscosity
Trait Class	Quality
Measurement Method	Measured with the Rapid Visco Analyzer (RVA)
Measurement Type	Unit
Measurement Unit	Pascal-second (Pa-s)

Softness of boiled cassava roots

Submitter

Name	Paula Iragaba
Program	National Crops Resources Research Institute (NaCRRI)

Request

Trait Name	Softness of boiled cassava roots
Definition	Mechanical attribute of boiled cassava roots relating to force required to make them compressed
Trait Class	Quality
Measurement Method	Use of a penetrometer to record the maximum force used to penetrate the boiled root
Measurement Type	Unit
Measurement Unit	Newton

Bemesia tabaci typo

Some biotic stress traits are named after Bemesia tabaci.
I think there is a typo and it should be Bemisia tabaci (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Bemisia+tabaci)

@aafolabi could you check and make the change of this is a typo.

Create: Rust disease incidence evaluation

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Creation Request

Trait Name	Rust disease incidence evaluation
Proposed Synonyms	Uromyces manihotis incidence
Definition	Proportion of plants in plot with Rust symptoms (Uromyces manihots)
Trait Class	Biotic Stress
Measurement Method	Disease incidence in plot
Measurement Type	Unit
Measurement Unit	%

Testing New Token

Submitter

Name	David Lyon
Program	BTI

Request

Trait Name	Testing New Token
Definition	Test Submission, please ignore
Trait Class	Morphological
Measurement Method	testing
Measurement Type	Unit
Measurement Unit	test

the chromometer variables are not linked to a scale

The following variables are not linked a scale

id: CO_334:0002064, name: b chromometer value
id: CO_334:0002065, name: L chromometer value
id: CO_334:0002066 name: a chromometer value

Textural characteristics of boiled roots in cassava

Texture characteristic Gradient of boiled cassava roots
Texture characteristic Max. Force of boiled cassava roots
Texture characteristic Distance at Max. Force of boiled cassava roots
Texture characteristic End force of boiled cassava roots
Texture characteristic Area under Curve of boiled cassava roots
Texture characteristic Linear Distance of boiled cassava roots

add scale to the variable male flower number counting on all levels

[Term]
id: CO_334:0000274
name: male flower number counting on all levels
namespace: CassavaVariable
def: "A count of the number male flowers after the buds appears, matures, and grows in size to become distinctive at all branching levels." []
synonym: "aflwmno" EXACT []
relationship: variable_of CO_334:0000403 ! Male flower number
relationship: variable_of CO_334:0010007 ! Counting:male flower number on all levels_method
created_by: aafolabi
creation_date: 2016-05-12T14:43:50Z

Second colon in term id causes AmiGO to not display correctly

Most of the CassavaScale terms are in the format CO_334:XXXXXXX:X. I believe the second colon in the id is invalid, or at the very least, AmiGO doesn't like it.

http://dev.planteome.org/amigo/search/ontology?q=*:*&fq=source:%22CassavaScale%22&sfq=document_category:%22ontology_class%22

Causes Amigo to not display the term name, but instead has a PURL link (that isn't valid).

Not sure if the issue is with AmiGO or the way the terms are numbered in the ontology, but my guess is the numbering isn't valid, so I'm putting the ticket here for it.

Note, I also found an errant quotation mark that I removed in commit 3349d85.

Rust disease incidence

Submitter

Name	Luciano Rogerio Braatz de Andrade
Program	EMBRAPA

Request

Trait Name	Rust disease incidence
Definition	Proportion of plants within a plot showing symptoms of Rust, (Uromyces manihotis Henn).
Trait Class	Biotic Stress
Measurement Method	Proportion of plants within a plot showing symptoms of Rust
Measurement Type	Unit
Measurement Unit	%

add method and scale to the variable assessment of apical pubescence boolean 0&1

[Term]
id: CO_334:0000256
name: assessment of apical pubescence boolean 0&1
namespace: CassavaVariable
def: "Assessment of the young leaf pubescence . Record the most frequent occurrence scored as 0 = Absent, 1 = Present." [CO:curators]
synonym: "APUBESA" RELATED []
relationship: variable_of CO_334:0000283 ! Apical Pubescence
created_by: AAfolabi
creation_date: 2015-09-28T17:48:12Z

add scale to the variable post-harvest physiological deterioration variable 0-10

[Term]
id: CO_334:0000077
name: post-harvest physiological deterioration variable 0-10
namespace: CassavaVariable
def: "Internal root discoloration or vascular streaking that renders cassava roots unfit for human or animal consumption.\nA number of root samples are cut into 7 slices and each slice is scored on a 0-10 scale." [CO:curators]
relationship: variable_of CO_334:0000266 ! post-harvest physiological deterioration
relationship: variable_of CO_334:0010001 ! Estimation: post-harvest physiological deterioration method

plot volume

Submitter

Name	anna van doorn
Program	Juelich

Request

Trait Name	plot volume
Definition	From Drone image analysis
The parameters from the distribution fit are unit less: shape and scale parameters are define has in: https://en.wikipedia.org/wiki/Weibull_distribution
Trait Class	Agronomic
Measurement Method	The volume is the sum of all z-values (the height of every point in the point cloud), times 0.01x0.01 (every pixel is 1 cm res)
Measurement Type	Unit
Measurement Unit	m3

Plant/plot height (m)

Submitter

Name	anna van doorn
Program	juelich

Request

Trait Name	Plant/plot height (m)
Definition	From drone image analysis:
The height is calculated from the mean of the 5% highest points in a plot point cloud (top 95 percentile)

 |

| Trait Class | Agronomic |
| Measurement Method | The height is calculated from the mean of the 5% highest points in a plot point cloud (top 95 percentile) |
| Measurement Type | Unit |
| Measurement Unit | meter |