# Phenome-Emphasis-Elixir: phenotyping data management and integration

Anne-Francoise Adam-Blondon, Cyril Pommier, Llorenç Cabrera Bosquet

► To cite this version:

Anne-Francoise Adam-Blondon, Cyril Pommier, Llorenç Cabrera Bosquet. Phenome-Emphasis-Elixir: phenotyping data management and integration. Interenational Grape Genetics and Breeding Symposium, Jul 2018, Bordeaux, France. pp.16. hal-02789613

HAL Id: hal-02789613

https://hal.inrae.fr/hal-02789613

Submitted on 5 Jun 2020

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# Phenome-Emphasis-Elixir: phenotyping
data management and integration

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A-F Adam-Blondon, C Pommier, L Cabrera-Bosquet

Grape Genetics and Breeding Symposium, Workshop on
grapevine phenotyping, France, Bordeaux, 2018 July 16-20th

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Genomic X Environment X Phenomic

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* Climate change adaptation

* Variety improvement

* Cultural Practices adaptations

* ...

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# Phenomic multidimensional data

PHENOME
Infrastructure Française
de Phénomique végétale
EMPHASIS

<figure><img src="image_14.png" /></figure>

PHIS

<figure><img src="image_15.png" /></figure>

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Data of air temperature weather station degree celsius

<figure><img src="image_17.png" /></figure>

http://www.phenome-fppn.fr/m3p/arch/2011/sa110013

http://www.phenome-fppn.fr/m3p/arch/2011/sa110014

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Soissons
x high N

Charger
x high N

Charger
x low
input

Soissons
x low
input

Soissons
x low
input

Soissons
x high N

Charger
x high N

Soissons
x high N

Soissons
x high N

<table><thead><tr><td>Genotype</td><td>traitement</td><td>Fusariose</td></tr></thead><tbody><tr><td>Soissons</td><td>low input</td><td>5</td></tr><tr><td>Soissons</td><td>high N</td><td>7</td></tr></tbody></table>

(b)

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Date

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INRA
SCIENCE & IMPACT
# Phenotyping Data in matrix, link with other types of data

Infrastructure Française
de Phénomique végétal

<figure><img src="image_23.png" /></figure>

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EURGI-GnpIS

<figure><img src="image_25.png" /><figcaption>Elaborated data</figcaption></figure>

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<table><thead><tr><td>Genotype</td><td>treatment</td><td>rep</td><td>LAI</td></tr></thead><tbody><tr><td>Soisson</td><td>fi</td><td>1</td><td>5</td></tr><tr><td>Soisson</td><td>fi</td><td>2</td><td>7</td></tr></tbody></table>

<table><thead><tr><td>Genotype</td><td>treatment</td><td>LAI</td></tr></thead><tbody><tr><td>Soisson</td><td>low input</td><td>6</td></tr></tbody></table>

<figure><img src="image_27.png" /></figure>

INRA
SCIENCE & IMPACT
# Strategy for data management

* Raw data

* Big in High through put platforms: Terabyte by experiment

* Difficult to obtain again and LT interest: long term storage

* No central Phenomic data archive

* Strategy: develop a federation of information system with central services

* Need for standards to support the federation

* Need for standard to support automatic data integration

PHENOME
Infrastructure Française
de Phénomique végétale
EMPHASIS

Portal

Web service

Databases

<figure><img src="image_28.png" /></figure>
# Federation of Plant phenotyping information systems

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* Easy to maintain

* Easy to improve in terms of functionalities for the user

Web User
interface

Web Service

Batch
Download

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# Plant Phenotyping Data Life cycle

EMPHASIS

Elixir

Following
experiments

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Phenotypic
analysis

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Data sharing
and Reuse

## TRAITS

- Tracking

- objects, events,
images

- Following

- plants, sensors,
cameras

- Environmental
conditions
Mapping/time
course

- Sensor calibration

- Data cleaning

- Calculated traits

- Time courses

- Spatial analysis

- Ratios (growth
per ...)

- Tools for data
quality

- Reproducible?

- Cross scale ?

- Modelling?

- From
measurements
to traits

- Tools for trait
quality

- heritability

- genetic
correlations

- Enable
reproducible
analyses (GxE,
GWAS, Genomic
Prediction, Evolution)

- Data integration
and linking

- Data Publication

- Data discovery

- Pipeline Hosting

I interoperable R Reusable

I interoperable R Reusable

R Reusable

F Iindable A Acessible I interoperable

F Iindable A Acessible I interoperable

I interoperable R Reusable

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Phenotype data in breeding

<table><thead><tr><th>Germplasm ID</th><th>PH</th><th>PH2</th><th>GCOL</th><th>GY</th></tr></thead><tbody><tr><td>24530</td><td>80</td><td>1</td><td>2</td><td>35</td></tr><tr><td>85432</td><td>120</td><td>3</td><td>3</td><td>48</td></tr><tr><td>78452</td><td>95</td><td>2</td><td>3</td><td>43</td></tr><tr><td>56093</td><td>100</td><td>2</td><td>1</td><td>50</td></tr></tbody></table>

1 VARIABLE

=

1 TRAIT + 1 METHOD + 1 SCALE

Woody Plant Ontology ONTOLOGY

Ontology name Woody Plant Ontology
Authors Célia Michotey
Version v1
Licence CC BY 4.0
Links CropOntology TVD5 format
Adonis format

## Traits, methods and scales

Search terms...

Woody Plant Ontology ONTOLOGY

Agronomical TRAIT CLASS

Fertility TRAIT CLASS

Morphological TRAIT CLASS

Other TRAIT CLASS

Phenological TRAIT CLASS

Physiological TRAIT CLASS

Quality TRAIT CLASS

Stress TRAIT CLASS

Stress: Abiotic stress TRAIT CLASS

Stress: Biotic stress TRAIT CLASS

Bacterial canker girdling index TRAIT

Bacterial canker lesion length TRAIT

Game damages TRAIT

Nests presence TRAIT

NID: Nests presence VARIABLE

## NID: Nests presence VARIABLE

Identifier WOODY:0000067

Name

NID

Synonyms Nests presence
NID[Adonis]

Context of use Trial evaluation

Status Standard for INRA

Institution INRA

Scientist Célia Michotey

Date 13/03/2017

Crop Woody Plant

## Nests presence TRAIT

Identifier WOODY:1000056

Name Nests presence

Description Presence or absence of nests

Main abbreviation NID

Status Standard for INRA

Class Stress: Biotic stress

## Visual scoring METHOD

Identifier WOODY:2000003

Name Visual scoring

Description Visual assessment with a reference scoring scale
Class Estimation

## Presence/ absence SCALE

Identifier WOODY:3000003

Name Presence/Absence

Data type Nominal

Decimal places 0

Min 0
# Variable identification: Plant height example

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Trait

+

Method

+

Unit

M1: Total height

M2: First tassel branch

M3: Last expanded leaf

M4: Youngest growing leaf

U1: cm

U2: mm

T1: Plant Height

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M5: Highest pixel
corresponding to plant

U3: pixel

...Allows as many combination as needed...

...Each trait, method and unit has to be identified

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# Object identification (URIs)

## URIs (Uniform Resource Identifiers)

⇒ standardized, unique, unambiguous identification of objects

0118

VARIETY PG_23

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SEEDLOT
ZM4388

ARCH2017-03-30

SCENARIO
WW
REP
Rep_1

XY
02_58

<caption>(a)</caption>

Prefix m3p: <http://phenome-fppn.fr/m3p>

**URI of plant**

<m3p:arch/2017/c17000118>

**URI of pot:**

<m3p:arch/2013/pc13001542>

**URI of cart:**

<m3p:arch/2013/ct1300123>

**URI of cabin:**

<m3p:arch/2018/ac180015>

**URI of camera:**

<m3p:arch/2018/ac180019>

<figure><img src="image_41.png" /></figure>

**URI of image:**

<m3p:arch/2017/ic17002295855>

<caption>(b)</caption>

Prefix diaphen: <http://phenome-fppn.fr/diaphen>

**URI of plot**

<diaphen:2017/o1700029>

**URI of plant:**

<diaphen:2017/17000147>

**URI of leaf:**

<diaphen:2017/117000590>

**URI of camera:**

<diaphen:2018/ac180002>

<figure><img src="image_42.png" /></figure>

**URI of image:**

<diaphen:2017/ic14001480237>

The same applies to infrastructure, sensors, people, **variables...**
# Annotation of events: plot and plant accidents

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Events or follow the **Web Annotation Data Model** that allows assigning motivation and purpose attributes to annotations (e.g. oa:describing, oa:identifying, oa:linking, oa: replying, etc.). **Dublin Core** properties such as dcterms:created or dcterms:creator are also used.
# Minimum Information About Plant Phenotyping Experiment

* Standard for metadata: data about the data set

* www.miappe.org

* Recently improved: detailed specification of the checklist and alignment with other existing standards, include needs of the forest trees community, ...

## Measures for interoperability of phenotypic data: minimum information requirements and formatting

Hanna Ćwiek-Kupczyńska, Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Ümit Seren, Björn Usadel, Stephan Weise, Paul Kersey and Paweł Krajewski

Plant Methods 2016 12:44

DOI: 10.1186/s13007-016-0144-4

© The Author(s) 2016

Received: 15 April 2016

Accepted: 18 October 2016

Published: 9 November 2016

trans

PLANT

PHENOME
Infrastructure PlantGenome
EMPHASIS

European
Plant
Phenotyping
Network

EPPN

accelerate

## Towards recommendations for metadata and data handling in plant phenotyping

<figure><img src="image_47.png" /></figure>

Paweł Krajewski¹,*, Dijun Chen², Hanna Ćwiek¹, Aalt D.J. van Dijk³, Fabio Fiorani⁴, Paul Kersey⁵, Christian Klukas², Matthias Lange², Augustyn Markiewicz⁶, Jan Peter Nap³, Jan van Oeveren⁷, Cyril Pommier⁸, Uwe Scholz², Marco van Schriek⁷, Björn Usadel⁴,⁹ and Stephan Weise²

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Author Affiliations

<< Previous | Next Article >>

Table of Contents

### This Article

J. Exp. Bot. (2015) 66 (18): 5417-5427.

doi: 10.1093/jxb/erv271

First published online: June 4, 2015

This article appears in:Special Issue: Phenotyping in Plants
# MIAPPE implementation: File Archive standard format

* ISA Tab for Phenotyping

* Investigation/Study/Assay

* Zip Archive

* MIAPPE Metadata

* Raw data

* Elaborated data

* Linked data / Metadata / Discovery data

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Data files
# MIAPPE implementation: Web Service

* Breeding API: International collaboration

* Servers implementations => **standard data exports**

* CGIARs international network: Integrated Breeding Platform

* Elixir Plant Community (GnpIS, CIRAD, ...)

* Emphasis Plant Community: (+PHIS, ...)

* Germinate (James Hutton Institute, UK)

* Clients implementations => **functionalities for users**

* Flapjack (JHI, UK): genotyping data visualization

* Search data in federations (URGI, EU)

* R analysis pipelines (CIP, Peru)

* Ontology Widget (URGI, FR)

* Diverse BrAPI Apps (USA) currently being developed for data visualisation

* Tools => **functionalities for data managers**

* BRAVA (IPK, D): validator of a BrAPI server implementation

* BrAPI to ISA-TAB; Batch downloads (ELIXIR, EU)

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Bill & Melinda Gates Foundation

CassavaBase

T3

IBP

JHI

Bioversity

CIRAD

INRA

IRRI

GOBII

Wageningen

CIP

DaRT

Cornell

iPlant

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The James
Hutton
Institute

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CGIAR

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Bioversity
International

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INRA
SCIENCE & IMPACT

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WAGENINGEN
UNIVERSITY & RESEARCH

www.brapi.org
# Federation(s) of Plant Information systems

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accelerate

PHENOME

Infrastructure Française de Phénomène végétal EMPHASIS

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## BrAPI-based portals

Web User
interface

<figure><img src="image_63.png" /></figure>

Web Service

<figure><img src="image_64.png" /></figure>

<figure><img src="image_65.png" /></figure>

Batch
Download

<figure><img src="image_66.png" /></figure>

INRA
SCIENCE & IMPACT
Aknowledgment & Questions

<figure><img src="image_67.png" /></figure>

<figure><img src="image_68.png" /></figure>

INRA
SCIENCE & IMPACT

<figure><img src="image_69.png" /></figure>

BrAPI

<figure><img src="image_70.png" /></figure>

iBET

<figure><img src="image_71.png" /></figure>

WAGENINGEN
UNIVERSITY & RESEARCH

<figure><img src="image_72.png" /></figure>

cirad

<figure><img src="image_73.png" /></figure>

<figure><img src="image_74.png" /></figure>

PHENOME
Infrastructure Française
de Phénomique végétal

<figure><img src="image_75.png" /></figure>

<figure><img src="image_76.png" /></figure>

<figure><img src="image_77.png" /></figure>

Crop Ontology
for agricultural data

<figure><img src="image_78.png" /></figure>

VIB

<figure><img src="image_79.png" /></figure>

Earlham
Institute

EMBL-EBI

<figure><img src="image_80.png" /></figure>

<figure><img src="image_81.png" /></figure>

trans

<figure><img src="image_82.png" /></figure>

<figure><img src="image_83.png" /></figure>

Biodiversity
International

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INRA
SCIENCE & IMPACT