Improving the annotations
Leo Valette
1, Julian Pietragalla
2, Marie-Angelique Laporte
1, Elizabeth
Arnaud
1Bioversity International
1, Integrated Breeding Platform
2•
Timeseries
•
Subsampling
•
Stress traits
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
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
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
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
Subsampling
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 »
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.
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:
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
?
?
Stress traits
-> symptoms
•
Damage, severity
•
Resitance
•
Tolerance
•
Response
•
Suceptibility
•
Recovery, survival/death
•
Number of plant showing symptoms, incidence
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 • Fungi • Bacteria • Virus • Nematode• Protozoa and algae
• Parasitic plant
• Environmental condition • Soil deficiency or excess • Water deficiency or excess
• Extreme temperature
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.