# WheatIS EWG annual meeting 2025

Michael Alaux

► To cite this version:

Michael Alaux. WheatIS EWG annual meeting 2025. PAG 32, Jan 2025, San Diego (CA), United States. hal-05528849

HAL Id: hal-05528849

https://hal.inrae.fr/hal-05528849v1

Submitted on 26 Feb 2026

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# WheatIS EWG annual meeting

* ✓ On site: please fill the participant list and photo agreement

* ✓ On Zoom: the session will be recorded. Feel free to turn off your camera if you don't want to appear on the record.

* ✓ I authorise the Wheat Initiative to take photographs and use, reuse, copy, publish, display, exhibit, license and distribute the materials in any promotional materials that relate to the Wheat Initiative which include university publications, catalogs, and website.

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wheatIS
WHEAT INFORMATION SYSTEM

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PAG'32

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# Agenda

- Round table and WheatIS news (10:00 - 10:15, Michael Alaux)

- Follow-up of AI at INRAE-URGI (10:15 – 10:30, Cyril Pommier)

- Machine learning to predict end-use quality in wheat (10:30 – 11:55, Muhammad Afzal, ECR travel awardee)

- AI in GrainGenes (11:55 - 11:20, Taner Sen)

- AI at University Western Australia (11:20 – 11:45, Dave Edwards)

- Plan for 2025 (budget, activities, ECRs) (11:45 - 12:00, Michael Alaux)

- Group photo

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Quick round table

☐ People on site only

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# WheatIS EWG memberships in 2024

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WHEAT
INITIATIVE

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<table><thead><tr><td>First Name</td><td>Last Name</td><td>EWG/ECR</td><td>Your role/position in your organisation</td><td>Country</td><td>Institution/Company</td><td>Year</td></tr></thead><tbody><tr><td>Michael</td><td>Alaux</td><td>EWG</td><td>Bioinformatics project manager</td><td>France</td><td>INRAE-URGI</td><td>2013</td></tr><tr><td>Ute</td><td>Baumann</td><td>EWG</td><td>Academic</td><td>Australia</td><td>University of Adelaide</td><td>2013</td></tr><tr><td>Mario</td><td>Caccamo</td><td>EWG</td><td>Head of Crop Bioinformatics</td><td>UK</td><td>NIAB</td><td>2013</td></tr><tr><td>Laurel</td><td>Cooper</td><td>EWG</td><td>Scientific Curator and Project C</td><td>USA</td><td>Oregon State University</td><td>2015</td></tr><tr><td>Robert</td><td>Davey</td><td>EWG</td><td>Group Leader</td><td>UK</td><td>Earlham Institute</td><td>2015</td></tr><tr><td>David</td><td>Edwards</td><td>EWG</td><td>Professor</td><td>Australia</td><td>University of Western Australia</td><td>2013</td></tr><tr><td>Gerard</td><td>Lazo</td><td>EWG</td><td>Geneticist, GrainGenes Curator</td><td>USA</td><td>United States of Agriculture, A</td><td>2013</td></tr><tr><td>Hadi</td><td>Quesneville</td><td>EWG</td><td>Research director / INRAE chief</td><td>France</td><td>INRAE</td><td>2013</td></tr><tr><td>Taner</td><td>Sen</td><td>EWG</td><td>Research Computational Biolog</td><td>USA</td><td>U.S. Department of Agriculture</td><td>2017</td></tr><tr><td>Saloni</td><td>Sharma</td><td>ECR</td><td>Post-doctoral researcher</td><td>India</td><td>National Agri-Food Biotechnol</td><td>2024</td></tr><tr><td>Sherry</td><td>Sun</td><td>ECR</td><td>Postgraduate Student</td><td>Canada</td><td>The University of British Colun</td><td>2024</td></tr><tr><td>Muhammad</td><td>Afzal</td><td>ECR</td><td>Postdoctoral Scientist</td><td>Germany</td><td>University of Hohenheim</td><td>02.06.2023</td></tr><tr><td>Bijendra</td><td>Khadka</td><td>ECR</td><td>Research Scientist PRP (Postdo</td><td>Canada</td><td>Agriculture and Agri-Food Car</td><td>12.06.2023</td></tr><tr><td>Cyril</td><td>Pommier</td><td>EWG</td><td>Leader of data federation servi</td><td>France</td><td>INRAE</td><td>2023</td></tr><tr><td>Manuel</td><td>Spannagl</td><td>EWG</td><td>Group Leader/PI</td><td>Germany</td><td>Helmholtz Center Munich</td><td>2023</td></tr><tr><td>Keywan</td><td>Hassani-Pak</td><td>EWG</td><td>Head of Bioinformatics / Found</td><td>UK</td><td>Rothamsted Research / Kneth</td><td>2023</td></tr><tr><td>Sarah</td><td>Dyer</td><td>EWG</td><td>Non-vertebrate Genomics Tear</td><td>UK</td><td>European Molecular Biology L</td><td>2023</td></tr><tr><td>Apoorv</td><td>Tiwari</td><td>ECR</td><td>Post-doctoral researcher</td><td>India</td><td>National Agri-food Biotechnol</td><td>13.09.2023</td></tr><tr><td>Weilong</td><td>Guo</td><td>EWG</td><td>Bioinformatics group leader</td><td>China</td><td>China Agricultural University</td><td>2023</td></tr><tr><td>Luis</td><td>Vargas Rojas</td><td>ECR</td><td>PhD candidate</td><td>USA</td><td>Purdue University</td><td>2024</td></tr></tbody></table>

EWG CHAIR AND CO-CHAIRS

<figure><img src="image_15.png" /><figcaption>Michael ALAUX
INRAE, France</figcaption></figure>

<figure><img src="image_16.png" /><figcaption>Mario CACCAMO
NIAB, UK</figcaption></figure>

<figure><img src="image_17.png" /><figcaption>Taner SEN
USDA-ARS, USA</figcaption></figure>

<figure><img src="image_18.png" /><figcaption>Sarah DYER
EMBL-EBI, UK</figcaption></figure>

<figure><img src="image_19.png" /><figcaption>Dave EDWARDS
University of WA
Australia</figcaption></figure>

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Highlights from 2024

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WHEAT
INITIATIVE

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# AI meeting

## Agenda

<table><tr><td>Welcome</td><td>Michael Alaux (INRAE-URGI)</td><td>4:00 PM</td></tr><tr><td>Testing BioCypher and BioChatter on our Neo4J knowledge graphs</td><td>Raphael Flores (INRAE-URGI)</td><td>4:05 PM - 4:30 PM</td></tr><tr><td>AI update from EMBL-EBI</td><td>Sarah Dyer (EMBL-EBI)</td><td>4:30 PM - 5 PM</td></tr><tr><td>Literature Review and GraphRAG in KnetMiner</td><td>Keywan Hassani-Pak (Rothamsted Research)</td><td>5 PM - 5:30 PM</td></tr><tr><td>AI update from GrainGenes</td><td>Taner Sen (GrainGenes)</td><td>Postponed to WheatIS annual meeting at PAG</td></tr><tr><td>LLM update from UWA</td><td>Dave Edwards (University of Western Australia)</td><td>Postponed to WheatIS annual meeting at PAG</td></tr></table>

* ✓ The main goal is to share ideas about AI

* ✓ I encourage as much discussion as possible

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WHEAT
INITIATIVE

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wheatIS
WHEAT INFORMATION SYSTEM

HD

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2024-10-1 14:00:15

WheatIS EWG half-yearly meeting AI

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Non répertoriée

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WHEAT
INITIATIVE

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wheatIS
WHEAT INFORMATION SYSTEM
☐ Any feedback from Dave or other attendees ?

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iwc 3RD INTERNATIONAL
WHEAT CONGRESS

22 - 27 September 2024 • Perth, Western Australia

Hosted by

MU Murdoch University

Centre for
Crop and Food
Innovation

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In Collaboration with

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GRDC
GRAINS RESEARCH
& DEVELOPMENT
CORPORATION

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WHEAT
INITIATIVE

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WHEAT
INITIATIVE

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# WheatIS data discovery tool

wheatIS
WHEAT INFORMATION SYSTEM

WHEAT

Home

Wheat@URGI

About

Join us

Terms of use

Help

News/Perspectives

## Data providers

**INRAE-URGI**
IWGSC@GnpIS [19,195,264]
GnpIS [624,827]
brapi@INRAE-URGI [15,949]
OpenMinTeD@GnpIS [1,692]
WheatIS File Repository [6]
Research Data Gouv [4]

**CAU**
TGT [5,041,169]
wGRN [270,235]
WheatUnion [105,200]
pNOGmap [118]

**EBI**
Ensembl Plants [1,954,199]

**Gramene**
Gramene Plants [1,954,199]

**IPK**
CR-EST [199,220]
GEBIS [51,820]
MetaCrop [355]
e!DAL - PGP Repository [144]

**T3**
The Triticeae Toolbox [206,406]
UniProt by T3 [16,607]

**UWA**
Wheat Pangenome [167,167]

**Rothamsted Research**
KnetMiner [108,474]

**GrainGenes**
GrainGenes [20,190]
Komugi wheat gene catalog by
GrainGenes [3,119]

**PGSB**
CrowsNest [13,324]

**CIMMYT**
Publications Repository [1,741]
Data Repository [374]

**EVA**
brapi@EVA [710]

**TERRA-REF**
brapi@TERRA-REF [284]

**IPGPAS**
PlantPhenoDB [6]

WheatIS
DataDiscovery

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Examples: yield, fhb

Search

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# WheatIS data discovery tool

## ☐ Changes overview

### ☐ Updates

☐ Gramene: done

☐ Ensembl Plants: done

☐ CIMMYT: done

### ☐ Addition of new databases

☐ DDBJ (Japan): done, but no wheat data at the moment

☐ e!DAL-PGP (IPK, Germany): done

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# WheatIS data discovery tool

## ☐ CIMMYT

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Communities & Collections All of DSpace ▼ Statistics

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Log In ▶

Home · CIMMYT · Wheat · First report of Fusarium re..

## First report of Fusarium redolens causing crown rot of wheat (Triticum spp.) in Turkey

CIMMYT

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CIMMYT R

(C)

CIMMYT Research Data & Software Repository Network > CIMMYT Research Data >

## 30th Elite Selection Wheat Yield Trial

Version 3.1

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Global Wheat Program; IWIN Collaborators; Singh, Ravi; Payne, Thomas, 2017. '30th Elite Selection Wheat Yield Trial', https://hdl.handle.net/11529/10404. CIMMYT Research Data & Software Repository Network. V3. UNF.6:eqPxHXkap6tCjpMDNPjjqQ-- [fileUNF]

Cite Dataset ▼

Learn about Data Citation Standards

Description 🔧

The Elite Selection Wheat Yield Trial (ESWYT) is a replicated yield trial that contains spring bread wheat (Triticum aestivum) germplasm adapted to Mega-environment 1 (ME1) which represents the optimally irrigated, low rainfall areas. Major stresses include leaf, stem and yellow rusts. Karnal bunt, and lodging. Representative areas include the Gangetic Valley (India), the Indus Valley (Pakistan), the Nile Valley (Egypt), irrigated river valleys in parts of China (e.g. Chengdu), and the Yaqui Valley (Mexico). This ME encompasses 36 million hectares spread primarily over Asia and Africa between 350S-350N latitudes. White (amber)-grained types are preferred by consumers of wheat in the vast majority of the areas. It is distributed to upto 200 locations and contains 50 entries. (2009)

Subject 🔧

Keyword 🔧

Agricultural Sciences

Agricultural research, Wheat, Triticum aestivum. Drought tolerance, Agronomic score. Heading time, Maturity time. Powdery mildew severity. Fusarium graminearum severity. Fusarium leaf blotch severity, Grain germination, Grain number per spike, Grain yield, Helminthosporium species severity, Spot blotch incidence, Tan spot severity, Lodging incidence, Stem rust coefficient of infection, Plant height. Leaf rust coefficient of infection, Stripe rust coefficient of infection. Stripe rust spike severity, Septoria blotch severity, Spike number, Spike length, Spikelet number, Septoria tritici blotch severity, Grain test weight, Grain weight, Winter kill damage, Mega Environment 1, 30th ESWYT, Selected check mark

Notes 🔧

IWIS2 Trial ID: 40807; Mega-environment: ME1 - Optimally irrigated, low rainfall environment

License/Data Use
Agreement

Custom Dataset Terms

Access Dataset ▼

Contact Owner

Share

Dataset Metrics 🔧

80g Downloads 🔧

Files

56885.pdf (46.4)

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Type

Article

Date

2015

Authors

Gebremariam, E.
Karakaya, A.
Erginbas Orakci
Dababat, A.A.
Sharma-Poudy,
Paulitz, T.C.

Access Rights

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Files

Metadata

Terms

Versions

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WHEAT
INITIATIVE
# WheatIS data discovery tool

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## e!DAL-PGP

e!DAL
 electronic data archive library

e!DAL - Plant Genomics and Phenomics Research Data Repository

IPK
 LEIBNIZ INSTITUTE

### Species

- [ ] Hordeum spontaneum [102]

- [ ] Triticum vulgare [46]

- [ ] Arabidopsis thaliana [2]

### Data type

- [ ] Sequencing Experiment [69]

- [ ] dataset [33]

- [ ] Phenotyping study [23]

- [ ] Genotyping Experiment [19]

### Database (28)

e!DAL - PGP Repository [144] x

Filter on Database...

### Data provider

- [ ] IPK [144]

Results 1 to 20 of 144

### Raw image files from an investigation conditions in a Hordeum vulgare

Phenotyping study

Hordeum spontaneum

This dataset contains 347442 raw image files of 2011-09-18. The vegetative biomass growth

... (expand)

### Variation data for a global diverse

Repository

Sequencing Experiment

Hordeum spontaneum

Variation matrices in VCF format are produced of 177 barley samples. Subsets of these

... (expand)

### BAC-based sequence scaffolds of

PGP Repository

Sequencing Experiment

Hordeum spontaneum

Genome sequence assemblies in FASTA based sequences (Mascher et al. 2017, N. ... (expand)

... (expand)

### Barley gene annotation file of

e!DAL - PGP Repository

Sequencing Experiment

Hordeum spontaneum

To avoid annotation artifacts due to fragmented sequences is nearly completely represented

... (expand)

**Citation:** K. Neumann (2017-11-09): Raw image files from an investigation of vegetative biomass growth in well-watered and drought stress conditions in a Hordeum vulgare set (2011-07-22 to 2011-09-18). DOI:10.5447/ipk/2017/25

↓ BibTeX

↓ RIS

↓ RDF/XML

↓ RDF/Turtle

↓ Text

↓ JSON-LD

**Abstract:** This dataset contains 347442 raw image files of a high-throughput plant phenotyping experiment, which was run from 2011-07-22 to 2011-09-18. The vegetative biomass growth of a small set of Hordeum vulgare plants has been monitored. The files are described using the ISA-Tab format and fulfill the MIAPPE recommendations. The raw images were processed by the barley analysis pipelines of the IAP software (version 1.1.2; https://doi.org/10.1104/pp.113.233932). The analysed results were exported in the '1130KN_IAP_export.xlsx' file.

**License:** CC0 1.0 Universal (Creative Commons Public Domain Dedication)

DOI: 10.5447/ipk/2017/25

Content: 63 Directories 348874 Files (555.9 GB)

**Files:**

//arendd@IPK-GATERSLEBEN.DE/Raw image files from an investigation of vegetative biomass growth in well-watered and drought stress conditions in a Hordeum vulgare set (2011-07-22 to 2011-09-18) [1 Directories 0 Files]

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Up to parent directory

1130KN

555.9 GB

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Download as ZIP

(NOTE: ZIP Extraction using the native Windows Zip Client can fail due to file path length, please use third-party ZIP client instead)

**Metadata**

<table><tr><td>CONTRIBUTOR:</td><td>Andreas Graner, Daniel Arend [Show full information]</td></tr><tr><td>CREATOR:</td><td>Kerstin Neumann [Show full information]</td></tr><tr><td>PUBLISHER:</td><td>e!DAL - Plant Genomics and Phenomics Research Data Repository (PGP), IPK Gatersleben, Seeland OT Gatersleben, Corrensstraße 3, 06466, Germany</td></tr><tr><td>SIZE:</td><td>555.9 GB</td></tr></table>

<table><tr><td>COVERAGE:</td><td>none</td></tr><tr><td>DATE:</td><td>Event: event<br/>UPDATED: TimePoint: Thu Nov 09 03:48:42 CET 2017<br/>CREATED: TimePoint: Wed Nov 08 16:31:22 CET 2017</td></tr><tr><td>LANGUAGE:</td><td>en</td></tr><tr><td>RELATION:</td><td>none</td></tr></table>

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WHEAT
INITIATIVE

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wheatIS
WHEAT INFORMATION SYSTEM

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# WheatIS data discovery tool

* Planned in 2025

* Major data updates

* PGSB

* Graingenes, KnetMiner, etc. ?

* Developments

* BrAPI v2

* Monitor outgoing traffic towards partner databases

* Display date of last data update
# Metrics for 2024

<table><thead><tr><th>2018</th><th>2019</th><th>2020</th><th>2021</th><th>2022</th><th>2023</th><th>2024</th></tr></thead><tbody><tr><td>3790</td><td>4639</td><td>7421</td><td>7814</td><td>8477</td><td>9894</td><td>11696</td></tr></tbody></table>

<table><thead><tr><th>Countries</th><th></th><th>Unique visitors</th><th>Number of visits</th><th>Pages</th></tr></thead><tbody><tr><td>China</td><td>cn</td><td>1,008 (27.1%)</td><td>1,584 (27.1%)</td><td>14,941</td></tr><tr><td>France</td><td>fr</td><td>575 (15.4%)</td><td>904 (15.5%)</td><td>9,009</td></tr><tr><td>United States</td><td>us</td><td>567 (15.2%)</td><td>891 (15.2%)</td><td>7,417</td></tr><tr><td>India</td><td>in</td><td>465 (12.5%)</td><td>731 (12.5%)</td><td>7,338</td></tr><tr><td>South Africa</td><td>za</td><td>189 (5.1%)</td><td>297 (5.1%)</td><td>3,054</td></tr><tr><td>Spain</td><td>es</td><td>90 (2.4%)</td><td>142 (2.4%)</td><td>1,481</td></tr><tr><td>Republic of Serbia</td><td>rs</td><td>69 (1.9%)</td><td>108 (1.8%)</td><td>1,118</td></tr><tr><td>Australia</td><td>au</td><td>74 (2.0%)</td><td>116 (2.0%)</td><td>1,094</td></tr><tr><td>Japan</td><td>jp</td><td>68 (1.8%)</td><td>106 (1.8%)</td><td>938</td></tr><tr><td>Germany</td><td>de</td><td>66 (1.8%)</td><td>103 (1.8%)</td><td>902</td></tr></tbody></table>

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WHEAT
INITIATIVE

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wheatIS
WHEAT INFORMATION SYSTEM

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Plan for 2025

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WHEAT
INITIATIVE

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wheatIS
WHEAT INFORMATION SYSTEM
# Activities for 2025

* Communication

* Update of the WheatIS website

* Social media: close X/Twitter and start LinkedIn ?

* WheatIS tutorial video with help of the Wheat Initiative

* Other activities we want to do together ?

* ECRs engagement (feedback from other EWGs, Sarah)

* Which follow-up to the AI meetings ?

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Budget request

☐ Up to 10 k€

☐ PAG meeting cost ~ 500 $

☐ Travel grant for PAG : 2 k€

☐ Feedback from awardee
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<figure><img src="image_86.png" /><figcaption>Group photo</figcaption></figure>