Crop Ontology model session-BRAINSTORMING.pptx

Full text

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Improving the annotations

Leo Valette

1

, Julian Pietragalla

2

, Marie-Angelique Laporte

1

, Elizabeth

Arnaud

1

Bioversity International

1

, Integrated Breeding Platform

2

(2)

Timeseries

Subsampling

Stress traits

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Variable as P+M+S

Property

Method

Scale

Administrative details

Environmental details

Crop management

details Experimental

factors

Time stamp Subsampling

Variable

Study metadata

Time and sampling stamp

Slide from Julian’s presentation of the BMS

(5)

Variable as P+M+S

Property

Method

Scale

Administrative details

Environmental details

Crop management

details Experimental

factors

Time stamp Subsampling

Variable

Study metadata

Time and sampling stamp

Slide from Julian’s presentation of the BMS

(6)

Variable as P+M+S

Plant height

Ruler

method

cm

Administrative details: PI name Institute Environmental details: From Field under drought experiment Crop management details: Irrigated Experimental factors: under low Nitrogen level Time stamp: at flowering Subsampling:

on plant 7

Variable

Study metadata

Time and sampling stamp

(7)

Timeseries

CROP SPECIFIC

Types of timestamps:

1. Absolute date

2. Phenological stage

3. Relative date from phenological stage

4. Relative date from observation

5. Relative date from agricultural practice

Time/Date unit

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Subsampling

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Entity

Quality

Experiment

Qualifier

relationship

Units

Environment

Genetic

Phenotype annotation

model

Source

Attribution

Who makes the assertion

Properties

When, what organization

Slide from George’s presentation: « Use of PATO and application in PhenomeNet »

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Assertion

E=panicle

(PO:0009049 ) (PATO:0000122 )

Q=length

Source:

PMID:20376514

G. Gkoutos

influences

Date: 10/05/2016

Organization: IBERS

Version: 1

DTH7

inheres_in

Annotation:

Phenotypes

in literature

Panicle length (PL) is an important trait for improving panicle

architecture and grain yield in rice (Oryza sativa L.). Three

populations were used to identify QTLs and candidate genes

associated with PL”

Panicle length was measured as the

length from the panicle neck to the

panicle tip of the main panicle.

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Description of

Mutant Phenotype

Atomized

Phenotype

statements

Entity

Quality

(PATO)

Dwarf with profuse

slender tillers, small

panicles

dwarf

PO: shoot system

decreased height

profuse tillers

PO: whole plant

has extra parts of type

(basal axillary shoot

system)

slender tillers

PO: basal axillary

shoot system

slender

small panicles

PO: inflorescence

decreased size

Delayed flowering;

Reduction in total

chlorophyll

GO: flowering

delayed

ChEBI: chlorophyll decreased concentration

PATO-based plant phenotype

annotation

Slide from George’s presentation:

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Trait decomposition into entity-attribute

Trait

Entity

Attribute

Plant height

Plant

Height

Number of secondary

branches

Secondary branch

Number

Flowering time

Plant

Flowering time

Phenotypic

acceptability

Plant

Phenotypic acceptability

Leaf chlorophyll

content

Leaf

Chlorophyll content

LAI

Leaf

One-sided area per

ground surface area

Barley leaf rust

severity

Plant

Barley leaf rust severity

Flour gluten content

Flour (milled grain)

Gluten content

Dough elasticity

Dough

Elasticity

Leafiness

?

?

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Stress traits

-> symptoms

Damage, severity

Resitance

Tolerance

Response

Suceptibility

Recovery, survival/death

Number of plant showing symptoms, incidence

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Causes

Symptoms/Signs

visible changes that occur in the host plant in response to a stress

Affected plant entities

Changes in the plant

entities

Growth stage

Phenological stage at which the symptom occurs

“Entity-attribute” traits

Trait 1

Trait 2

Trait 3

….

Is phenotype of

Stress

Stressor/Causal agent

• Pathogen • FungiBacteriaVirus • Nematode

• Protozoa and algae

• Parasitic plant

Environmental conditionSoil deficiency or excess • Water deficiency or excess

• Extreme temperature

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Resistance

Plant ability to reduce or suppress the stressor negative effects

Damage (or injury)

Extent of the symptoms that negatively impact the development of the plant

Tolerance

Plant ability to withstand or endure stressful conditions. Unlike for “resistance”, the stress persists

Recovery

Ability to develop normally

(disappearance of the symptoms) after a stress event.

Severity

Extent of the damage

Response

Is the host reaction to a stress characterized by the

expression of symptoms

Incidence

Proportion of plants in the plot showing symptoms

Disease

incubation/developm

ent/

evolution time

Time elapsed between the appearance of initial

symptoms and latest symptoms.

Number of plant

showing symptoms

Symptom (or sign) intensity (or extent)

Can for instance be the disease count i.e. the number of lesions (or other units of infection) per plant or per area of plant tissue per plant or per area of plant tissue.

Number of plant

entities showing

symptoms

Susceptibility

type of reaction of a host to a stress factor.

Survival/Death

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Curation example: cold tolerance

1 Trait :« ability of the plant to grow

normally under cold conditions »

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Curation example: cold tolerance

Differences explained in method and scale

« Observe the

vigor

,

leaf colour

and

damage to seedlings

« Observe effects on

spikelet fertility, heading and

growth

« effects on

vigour

and

leaf colour

of plants grown at 17-18

degrees C

before flowering

« Experimental materials with more than 60 % of seeds

with coleoptile

length ≥ 5 mm

are selected as tolerant”

7-9= Sensitive=

yellowing

or

brownish of almost all leaves

and dead

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Curation example: cold tolerance

Minimal information:

Stressor

Figure

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References

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Related subjects : Ontology model