<figure><img src="image_1.png" /></figure>

HAL
open science

# Feedback from the wheat community: the case of the WheatIS

Michael Alaux

► To cite this version:

Michael Alaux. Feedback from the wheat community: the case of the WheatIS. Grapedia kickoff meeting, Nov 2022, Online, Spain. hal-04536615

HAL Id: hal-04536615

https://hal.inrae.fr/hal-04536615

Submitted on 8 Apr 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_1.png" /></figure>

# Feedback from the wheat community:
the case of the WheatIS

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

Michael Alaux, 23 November 2022

<figure><img src="image_4.png" /></figure>

RÉPUBLIQUE
FRANÇAISE

Liberté
Egalité
Fraternité

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>
<figure><img src="image_3.png" /></figure>

# Feedback from the wheat community:
the case of the WheatIS

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

Michael Alaux, 23 November 2022

<figure><img src="image_6.png" /></figure>

RÉPUBLIQUE
FRANÇAISE

Liberté

Egalité

Fraternité

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>
# Outline

- The Wheat Initiative

- The WheatIS Expert Working Group

- Data standards

- Data discovery
# Outline

- The Wheat Initiative

- The WheatIS Expert Working Group

- Data standards

- Data discovery
The Wheat Initiative

<figure><img src="image_9.png" /></figure>

https://www.wheatinitiative.org
The Wheat Initiative

<figure><img src="image_11.png" /></figure>

https://www.wheatinitiative.org
Background

☐ Proposed by research and funding organisations from several countries

- ☐ Endorsed by the G20 Agricultural Ministers to contribute to improving world food security

☐ Launched on 15 September 2011

<figure><img src="image_10.png" /></figure>
Background

- Proposed by research and funding organisations from several countries

- Endorsed by the G20 Agricultural Ministers to contribute to improving world food security

- Launched on 15 September 2011

<figure><img src="image_12.png" /></figure>
# Challenges and vision

☐ The world wheat production is not meeting the necessary future demand:

• food demand will increase by 60% by 2050, while yields are stagnating

• wheat is particularly susceptible to climate change.

☐ Support the development of a global wheat public-private research community sharing resources, data, knowledge to improve wheat productivity, quality and sustainable production around the world.
# Challenges and vision

□ The world wheat production is not meeting the necessary future demand:

• food demand will increase by 60% by 2050, while yields are stagnating

• wheat is particularly susceptible to climate change.

□ Support the development of a global wheat public-private research community sharing resources, data, knowledge to improve wheat productivity, quality and sustainable production around the world.
Strategic Research Agenda

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

WHEAT
INITIATIVE

July 2022

Open Access

Feature Paper

Review

Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative

by ⬒ Peter Langridge 1,2,* ⬒, ⚙ Michael Alaux 3, ⚙ Nuno Felipe Almeida 4 ⬒, ⚙ Karim Ammar 5,

✉️ Michael Baum 6, ✉️ Faouzi Bekkaoui 7, ✉️ Alison R. Bentley 5 ⚙, ✉️ Brian L. Beres 8 ⚙,

✉️ Bettina Berger 9 ⚙, ✉️ Hans-Joachim Braun 5, ✉️ Gina Brown-Guedira 10 ⚙,

✉️ Christopher James Burt 11, ✉️ Mario Jose Caccamo 12 ⚙, ✉️ Luigi Cattivelli 13 ⚙, ✉️ Gilles Charmet 14,

✉️ Peter Civán 14, ✉️ Sylvie Cloutier 15 ⚙, ✉️ Jean-Pierre Cohan 16, ✉️ Pierre J. Devaux 17 ⚙,

✉️ Fiona M. Doohan 18, + Show full author list

Agronomy **2022**, *12*(11), 2767; https://doi.org/10.3390/agronomy12112767

Received: 26 September 2022 / Revised: 28 October 2022 / Accepted: 29 October 2022 /

Published: 7 November 2022

https://doi.org/10.3390/agronomy12112767

<footnote n="1">¹ School of Agriculture, Food and Wine, Waite Campus, University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia</footnote>

<footnote n="2">² Wheat Initiative, JKI (Julius Kühn Institute), Federal Research Centre for Cultivated Plants, 14195 Berlin, Germany</footnote>

<footnote n="3">³ INRAE, URGI, Université Paris-Saclay, 78026 Versailles, France</footnote>

<footnote n="4">⁴ ASUR Plant Breeding, 60190 Estrées-Saint-Denis, France</footnote>

<footnote n="5">⁵ CIMMYT (International Maize and Wheat Improvement Center), Texcoco 56237, Mexico</footnote>

<footnote n="6">⁶ ICARDA (International Center for Agricultural Research in the Dry Areas), Rabat 10106, Morocco</footnote>

<footnote n="7">⁷ INRA (National Institute for Agricultural Research), Rabat 10090, Morocco</footnote>

<footnote n="8">⁸ AAFC (Agriculture & Agri-Food Canada), Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada</footnote>

<footnote n="9">⁹ Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA 5064, Australia</footnote>

<footnote n="10">¹⁰USDA-ARS (United States Department of Agriculture—Agricultural Research Service), Plant Science Research, Raleigh, NC 27695, USA</footnote>

<footnote>+ Show full affiliation list</footnote>

<footnote>* Author to whom correspondence should be addressed.</footnote>
# Strategic Research Agenda

STRATEGIC RESEARCH
AGENDA

<figure><img src="image_13.png" /></figure>

WHEAT
INITIATIVE

July 2022

Open Access

Feature Paper

Review

## Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative

by ⬒ Peter Langridge <fnref n="1" />,<fnref n="2" />,* ⬒, ⚙ Michael Alaux <fnref n="3" />, ⚙ Nuno Felipe Almeida <fnref n="4" /> ⬒, ⚙ Karim Ammar <fnref n="5" />,

✉️ Michael Baum <fnref n="6" />, ✉️ Faouzi Bekkaoui <fnref n="7" />, ✉️ Alison R. Bentley <fnref n="5" /> ⚙, ✉️ Brian L. Beres <fnref n="8" /> ⚙,

✉️ Bettina Berger <fnref n="9" /> ⚙, ✉️ Hans-Joachim Braun <fnref n="5" />, ✉️ Gina Brown-Guedira <fnref n="10" /> ⚙,

✉️ Christopher James Burt ¹¹, ✉️ Mario Jose Caccamo ¹² ⚙, ✉️ Luigi Cattivelli ¹³ ⚙, ✉️ Gilles Charmet ¹⁴,

✉️ Peter Civán ¹⁴, ✉️ Sylvie Cloutier ¹⁵ ⚙, ✉️ Jean-Pierre Cohan ¹⁶, ✉️ Pierre J. Devaux ¹⁷ ⚙,

✉️ Fiona M. Doohan ¹⁸, + Show full author list

Agronomy **2022**, *12*(11), 2767; https://doi.org/10.3390/agronomy12112767

Received: 26 September 2022 / Revised: 28 October 2022 / Accepted: 29 October 2022 /

Published: 7 November 2022

https://doi.org/10.3390/agronomy12112767

<footnote n="1">¹ School of Agriculture, Food and Wine, Waite Campus, University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia</footnote>

<footnote n="2">² Wheat Initiative, JKI (Julius Kühn Institute), Federal Research Centre for Cultivated Plants, 14195 Berlin, Germany</footnote>

<footnote n="3">³ INRAE, URGI, Université Paris-Saclay, 78026 Versailles, France</footnote>

<footnote n="4">⁴ ASUR Plant Breeding, 60190 Estrées-Saint-Denis, France</footnote>

<footnote n="5">⁵ CIMMYT (International Maize and Wheat Improvement Center), Texcoco 56237, Mexico</footnote>

<footnote n="6">⁶ ICARDA (International Center for Agricultural Research in the Dry Areas), Rabat 10106, Morocco</footnote>

<footnote n="7">⁷ INRA (National Institute for Agricultural Research), Rabat 10090, Morocco</footnote>

<footnote n="8">⁸ AAFC (Agriculture & Agri-Food Canada), Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada</footnote>

<footnote n="9">⁹ Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA 5064, Australia</footnote>

<footnote n="10">¹⁰USDA-ARS (United States Department of Agriculture—Agricultural Research Service), Plant Science Research, Raleigh, NC 27695, USA</footnote>

<footnote>+ Show full affiliation list</footnote>

<footnote>* Author to whom correspondence should be addressed.</footnote>
# Organisation

WHEAT INITIATIVE SECRETARIAT

WHEAT INITIATIVE MEMBERS

MEMBER
STATES

INTERNATIONAL
ORGANISATIONS

INDUSTRY

INSTITUTION'S
COORDINATION
COMMITTEE

RESEARCH
COMMITTEE

SCIENTIFIC
BOARD

EXPERT WORKING GROUPS

ABIOTIC STRESS

BREEDING

GERMPLASM

PESTS

DURUM

QUALITY

NUTRIENT

AGRONOMY

PHENOTYPING

WHEAT IS

FUNDING

PATHOGENS

ASSOCIATED PROGRAMMES

IWGSC

IWYP

AgMIP

10+ GENOMES

WheatBi

WHEAT INITIATIVE PROGRAMMES

AHEAD

WheatVIVO

WheatIS

Reference
Collection

NUMBERS

11 Expert Working
Groups (EWG)

14 member countries
(public)

2 research organisations

5 Associated Programmes

600+ EWG members

5 industry members
(private)

5 observer countries

<figure><img src="image_13.png" /></figure>

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

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

<figure><img src="image_16.png" /></figure>
# Organisation

WHEAT INITIATIVE SECRETARIAT

WHEAT INITIATIVE MEMBERS

MEMBER
STATES

INTERNATIONAL
ORGANISATIONS

INDUSTRY

INSTITUTION'S
COORDINATION
COMMITTEE

RESEARCH
COMMITTEE

SCIENTIFIC
BOARD

EXPERT WORKING GROUPS

ABIOTIC STRESS

BREEDING

GERMPLASM

PESTS

DURUM

QUALITY

NUTRIENT

AGRONOMY

PHENOTYPING

WHEAT IS

FUNDING

PATHOGENS

ASSOCIATED PROGRAMMES

IWGSC

IWYP

AgMIP

10+ GENOMES

WheatBi

WHEAT INITIATIVE PROGRAMMES

AHEAD

WheatVIVO

WheatIS

Reference
Collection

## NUMBERS

11 Expert Working
Groups (EWG)

14 member countries
(public)

2 research organisations

5 Associated Programmes

600+ EWG members

5 industry members
(private)

5 observer countries

<figure><img src="image_14.png" /></figure>
The Wheat Information System
Expert Working Group

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

wheat

WHEAT INFORMATION SYSTEM

http://www.wheatis.org/
# The Wheat Information System
## Expert Working Group

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

wheatIS
WHEAT INFORMATION SYSTEM

http://www.wheatis.org/
# Community

- ☐ Building an expert working group

- ☐ Seeking help from other communities (RDA)

- ☐ Surveys

- ☐ Fundings for meetings

- ☐ A successful result

- ☐ Outreach

<figure><img src="image_18.png" /></figure>

**Abstract**

The International Wheat Information System (WheatIS) Expert Working Group (EWG) was initiated in 2012 under the Wheat Initiative with a broad range of contributing organizations. The mission of the WheatIS EWG was to create an informational infrastructure, establish data standards, and build a single portal that allows search, retrieval, and display of globally distributed wheat data sets that are indexed in standard data formats at servers around the world. The web portal at WheatIS.org was released publicly in 2015, and by 2020, it expanded to 8 geographically-distributed nodes and around 20 organizations under its umbrella.

In this paper, we present our experience, the challenges we faced, and the answer we brought for establishing an international research community to build an informational infrastructure. Our hope is that our experience with building wheatis.org will guide current and future research communities to facilitate institutional and international challenges to create global tools and resources to help their respective scientific communities.

https://doi.org/10.12688/f1000research.23525.1
# Community

- ☐ Building an expert working group

- ☐ Seeking help from other communities (RDA)

- ☐ Surveys

- ☐ Fundings for meetings

- ☐ A successful result

- ☐ Outreach

<figure><img src="image_16.png" /></figure>

**Abstract**

The International Wheat Information System (WheatIS) Expert Working Group (EWG) was initiated in 2012 under the Wheat Initiative with a broad range of contributing organizations. The mission of the WheatIS EWG was to create an informational infrastructure, establish data standards, and build a single portal that allows search, retrieval, and display of globally distributed wheat data sets that are indexed in standard data formats at servers around the world. The web portal at WheatIS.org was released publicly in 2015, and by 2020, it expanded to 8 geographically-distributed nodes and around 20 organizations under its umbrella.

In this paper, we present our experience, the challenges we faced, and the answer we brought for establishing an international research community to build an informational infrastructure. Our hope is that our experience with building wheatis.org will guide current and future research communities to facilitate institutional and international challenges to create global tools and resources to help their respective scientific communities.

https://doi.org/10.12688/f1000research.23525.1
About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

wheatIS
WHEAT INFORMATION SYSTEM

<figure><img src="image_19.png" /></figure>

## About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

**Help desk:** If you have questions regarding this Wheat Information System project, please contact wheatis-contact@wheatis.org

Tweets by @WheatIS

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

<figure><img src="image_22.png" /></figure>

1

2

3

4

WheatIS

An International Wheat Information System

An international wheat information system for general, scientific and research purposes.

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

<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>

5

<figure><img src="image_26.png" /></figure>

6

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

7

<figure><img src="image_28.png" /></figure>
About

Collaborators

Search

Data Standards

Submit Data

Tools

Links

WheatIS Nodes

WheatIS

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

wheatIS

WHEAT INFORMATION SYSTEM

## About

This project aims at building an International Wheat Information System, called hereafter WheatIS, to support the wheat research community. The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools.

This project is based on the principles listed below:

* Collective building of the WheatIS to better respond to the needs of the international wheat community;

* Incremental implementation to offer rapidly an operational information system;

* Emphasis on Quality Assurance to serve as a framework for an approach with incremental implementation;

* Promotion of an open-access model for data exchange;

* Reliance on a distributed system;

* Use of Virtual Machine and Cloud Computing technologies to facilitate sharing data and tools;

* Promotion of the visibility of each participating platform to contribute to their sustainability.

If you have questions regarding this Wheat Information System project, please contact: wheatis-contact@wheatis.org

**Help desk:** If you have questions regarding this Wheat Information System project, please contact wheatis-contact@wheatis.org

Tweets by @WheatIS

<figure><img src="image_18.png" /></figure>
Data standards

<figure><img src="image_29.png" /></figure>

RESEARCH DATA ALLIANCE
Data standards

<figure><img src="image_19.png" /></figure>

RESEARCH DATA ALLIANCE
# RDA Wheat Data Interoperability Working Group

- ☐ Building on existing standards and practices

- ☐ Converging towards the recommendations

- ☐ Dissemination

- Website

- Agroportal for wheat ontologies

- ☐ Adoption

<figure><img src="image_30.png" /></figure>

https://doi.org/10.12688/f1000research.12234.2
# RDA Wheat Data Interoperability Working Group

- ☐ Building on existing standards and practices

- ☐ Converging towards the recommendations

- ☐ Dissemination

- Website

- Agroportal for wheat ontologies

- ☐ Adoption

<figure><img src="image_20.png" /></figure>

https://doi.org/10.12688/f1000research.12234.2
## Wheat Data Interoperability Guidelines

Home

Guidelines

<figure><img src="image_31.png" /></figure>

Ontologies & Vocabularies

Use cases

<figure><img src="image_32.png" /></figure>

Getting involved

About

<figure><img src="image_33.png" /></figure>

<figure><img src="image_34.png" /></figure>

## Welcome

These recommendations have been prepared by members of the Wheat Data Interoperability Working Group (WG), one of the WGs of the Research Data Alliance and the only WG of the Agriculture Data Interoperability Interest Group. The group is coordinated by members of the Wheat Initiative, a global initiative that aims to reinforce synergies between bread and durum wheat national and international research programmes to increase food security, nutritional value and safety while taking into account societal demands for sustainable and resilient agricultural production systems. All the standards and databases presented in these recommendations are referenced into the FAIRsharing website.

More specifically, the WG aims to:

<figure><img src="image_35.png" /></figure>

**Promote** the adoption of common standards, vocabularies and best practices for Wheat data management

<figure><img src="image_36.png" /></figure>

**Facilitate** access, discovery and reuse of wheat data

<figure><img src="image_37.png" /></figure>

**Facilitate** wheat data integration

## Guidelines

Under the submenus of this section you will find information on the best practices, tools, recommendations and examples to create, manage and share data related to Wheat. It includes subsections for each of the following data types:

What are currently the most used and relevant vocabularies in the context of Wheat Initiative?

Sequ

Gene

Phen

Germ

Gene

Phys

Exempl

From December to 2014 to January 2015 the editorial team conducted a survey "Towards a Comprehensive Overview of Ontologies and Vocabularies for Research on Wheat". The objective was to collect information about the visibility, interoperability, domain, content and other technical aspects of relevant ontologies and vocabularies. As a result, in February 2015 a report (link) was published, and also a list of vocabularies listed as follows:

1. AGROVOC

2. Biorefinery

3. CAB Thesaurus (CABT)

4. Cell Ontology (CL)

5. Chemical Entities of Biological Interest (ChEBI)

6. Crop Ontology (CO)

7. Crop Research Ontology - part of Crop Ontology (CO_715)

8. Environment Ontology (ENVO)

9. Experimental Factor Ontology (EFO)

10. Feature Annotation Location Description Ontology (FALDO)

11. NAL Thesaurus (NALT)

12. Phenotype And Trait Ontology (PATO)

13. Plant Experimental Conditions Ontology (Plant Environment Ontology, EO, may be changing to PECO)

Links

FAIRshare

## Use cases

<figure><img src="image_38.png" /></figure>

Clic on the titles for details

1. QUERY ON TRIAL DATA ASSOCIATED WITH VARIETIES

2. DECIPIER THE EFFECT OF SNPS

3. IDENTIFICATION OF WHEAT GENES THAT CONTROL ROOT GROWTH

4. QUERY DATA BY GERMPLASM/GENOTYPE

5. QUERY PHENOTYPE TRIALS TO BUILD INTEGRATIVE DATASET FOR PHENOTYPE OR GENETIC ANALYSIS.

6. QUERY ON GERMPLASM WITH SPECIFIC TRAITS
## Wheat Data Interoperability Guidelines

Home

Guidelines

Ontologies & Vocabularies

Use cases

Getting involved

About

<figure><img src="image_21.png" /></figure>

## Welcome

These recommendations have been prepared by members of the Wheat Data Interoperability Working Group (WG), one of the WGs of the Research Data Alliance and the only WG of the Agriculture Data Interoperability Interest Group. The group is coordinated by members of the Wheat Initiative, a global initiative that aims to reinforce synergies between bread and durum wheat national and international research programmes to increase food security, nutritional value and safety while taking into account societal demands for sustainable and resilient agricultural production systems. All the standards and databases presented in these recommendations are referenced into the FAIRsharing website.

More specifically, the WG aims to:

<figure><img src="image_22.png" /></figure>

**Promote** the adoption of common standards, vocabularies and best practices for Wheat data management

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

**Facilitate** access, discovery and reuse of wheat data

<figure><img src="image_24.png" /></figure>

**Facilitate** wheat data integration

## Guidelines

Under the submenus of this section you will find information on the best practices, tools, recommendations and examples to create, manage and share data related to Wheat. It includes subsections for each of the following data

types: What are currently the most used and relevant vocabularies in the context of Wheat Initiative?

Sequ

Gene

Phen

Germ

Gene

Phys

Exempl

From December 2014 to January 2015 the editorial team conducted a survey "Towards a Comprehensive Overview of Ontologies and Vocabularies for Research on Wheat". The objective was to collect information about the visibility, interoperability, domain, content and other technical aspects of relevant ontologies and vocabularies. As a result, in February 2015 a report (link) was published, and also a list of vocabularies listed as follows:

1. AGROVOC

2. Biorefinery

3. CAB Thesaurus (CABT)

4. Cell Ontology (CL)

5. Chemical Entities of Biological Interest (ChEBI)

6. Crop Ontology (CO)

7. Crop Research Ontology - part of Crop Ontology (CO_715)

8. Environment Ontology (ENVO)

9. Experimental Factor Ontology (EFO)

10. Feature Annotation Location Description Ontology (FALDO)

11. NAL Thesaurus (NALT)

12. Phenotype And Trait Ontology (PATO)

13. Plant Experimental Conditions Ontology (Plant Environment Ontology, EO, may be changing to PECO)

Links

FAIRshare

## Use cases

<figure><img src="image_25.png" /></figure>

Clic on the titles for details

1. QUERY ON TRIAL DATA ASSOCIATED WITH VARIETIES

2. DECIPIER THE EFFECT OF SNPS

3. IDENTIFICATION OF WHEAT GENES THAT CONTROL ROOT GROWTH

4. QUERY DATA BY GERMPLASM/GENOTYPE

5. QUERY PHENOTYPE TRIALS TO BUILD INTEGRATIVE DATASET FOR PHENOTYPE OR GENETIC ANALYSIS.

6. QUERY ON GERMPLASM WITH SPECIFIC TRAITS
Data discovery

wheatIS
WHEAT INFORMATION SYSTEM

WHEAT
INITIATIVE

<figure><img src="image_39.png" /></figure>

WheatIS
DataDiscovery

Exemples : yield, fhb

Rechercher

https://urgi.versailles.inrae.fr/wheatis
Data discovery

wheatIS

WHEAT INFORMATION SYSTEM

WHEAT
INITIATIVE

<figure><img src="image_26.png" /></figure>

WheatIS
DataDiscovery

Exemples : yield, fhb

Rechercher

https://urgi.versailles.inrae.fr/wheatis
# Federated data portal

<figure><img src="image_40.png" /></figure>

The WheatIS
Data
Discovery

One generic portal searching
all the metadata and linking
back to each source repository
# Federated data portal

## The WheatIS Data Discovery

One generic portal searching all the metadata and linking back to each source repository

THE UNIVERSITY OF WESTERN AUSTRALIA

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

## INRAE-URGI

IWGSC@GnpIS [19 195 264]

GnpIS [631 498]

brapi@INRAE-URGI [15 949]

OpenMinTeD@GnpIS [1 692]

WheatIS File Repository [6]

## EBI

Ensembl Plants [3 071 189]

## IPK

CR-EST [199 220]

GEBIS [51 820]

MetaCrop [355]

## Gramene

Gramene [229 851]

## 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

CIMMYT Publications [1 600]

CIMMYT Datasets [183]

## EVA

brapi@EVA [710]

## TERRA-REF

brapi@TERRA-REF [284]

## IPGPAS

PlantPhenoDB [6]
# Repositories

## INRAE-URGI

IWGSC@GnpIS [19 195 264]

GnpIS [631 498]

brapi@INRAE-URGI [15 949]

OpenMinTeD@GnpIS [1 692]

WheatIS File Repository [6]

## EBI

Ensembl Plants [3 071 189]

## IPK

CR-EST [199 220]

GEBIS [51 820]

MetaCrop [355]

## Gramene

Gramene [229 851]

## 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

CIMMYT Publications [1 600]

CIMMYT Datasets [183]

## EVA

brapi@EVA [710]

## TERRA-REF

brapi@TERRA-REF [284]

## IPGPAS

PlantPhenoDB [6]
Behind the scene

<figure><img src="image_41.png" /></figure>
# Behind the scene

<figure><img src="image_28.png" /></figure>
# Behind the scene

## International Network

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

## Multiple Data Sources

<figure><img src="image_43.png" /></figure>

Extract/Transform

<figure><img src="image_44.png" /></figure>
# Behind the scene

## International Network

<figure><img src="image_29.png" /></figure>

## Multiple Data Sources

<figure><img src="image_30.png" /></figure>

Extract/Transform

<figure><img src="image_31.png" /></figure>
# Behind the scene

<figure><img src="image_45.png" /></figure>
# Behind the scene

<figure><img src="image_32.png" /></figure>
Behind the scene

<figure><img src="image_46.png" /></figure>
# Behind the scene

International Network

France

<figure><img src="image_33.png" /></figure>

SouthGreen
bioinformatics platform

arcad
Crop biometry research and data center

PHENOME
FPPN

<figure><img src="image_34.png" /></figure>

MaiAGE
MaiAGE is the new name of CIMMYT.

Germany

<figure><img src="image_35.png" /></figure>

HELMHOLTZ
GEMEINSCHAFT

<figure><img src="image_36.png" /></figure>

IPK
GATERSLEBEN

PLANTS DB

United Kingdom

<figure><img src="image_37.png" /></figure>

EnsemblPlants

<figure><img src="image_38.png" /></figure>

ROTHAMSTED
RESEARCH

EMBL-EBI

<figure><img src="image_39.png" /></figure>

TGAC

The Genome Analysis Centre™

United States

USDA

NIFA

<figure><img src="image_40.png" /></figure>

Triticace CAP

GrainGenes
A Database for Triticace and Avena

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

Gramene

Australia

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

THE UNIVERSITY OF
WESTERN
AUSTRALIA

Mexico

<figure><img src="image_43.png" /></figure>

CIMMYT

International Maize and Wheat Improvement Center

Multiple Data Sources

<figure><img src="image_44.png" /></figure>

```json
{
  "entryType": "Bibliography",
  "node": "CIMMYT",
  "databaseName": "CIMMYT Publications",
  "description": "Genetic analysis and mapping ...",
  "url": "http://hdl.handle.net/10883/2969",
  "species": [
    "Septoria tritici blotch",
    "Triticum aestivum 1.",
    "Wheat"
  ],
  "name": "10883/2969"
}
```

Extract/Transform

<figure><img src="image_45.png" /></figure>

JSON Files

<figure><img src="image_46.png" /></figure>
# Behind the scene

<figure><img src="image_47.png" /></figure>
Behind the scene

<figure><img src="image_47.png" /></figure>
# Behind the scene

<figure><img src="image_48.png" /></figure>
# Behind the scene

<figure><img src="image_48.png" /></figure>
# Behind the scene

<figure><img src="image_49.png" /></figure>
# Behind the scene

<figure><img src="image_49.png" /></figure>
<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /></figure>

# Data exchange format

<table><thead><tr><td>Field</td></tr></thead><tbody><tr><td><ul><li>name</li><li>url</li><li>description</li><li>entryType</li><li>species</li><li>node</li><li>databaseName</li></ul></td></tr></tbody></table>

<table><thead><tr><td>Status</td></tr></thead><tbody><tr><td><ul><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li></ul></td></tr></tbody></table>

<table><thead><tr><td>Cardinality</td></tr></thead><tbody><tr><td><ul><li>1</li><li>1</li><li>1</li><li>1</li><li>1-*</li><li>1</li><li>1</li></ul></td></tr></tbody></table>

<table><thead><tr><td>Constraints</td></tr></thead><tbody><tr><td><ul><li>unique</li><li>none</li><li>none</li><li>cf. list in doc, recom.</li><li>cf. Species list below</li><li>same for all a dataset</li><li>none</li></ul></td></tr></tbody></table>

* WheatIS species list: Aegilops*, Hordeum*, Triticum*, Wheat*

* Format: JSON or TSV, as you wish!

* Web server: HTTP of FTP, as you wish!

* The up-to-date format is always available at https://urgi.versailles.inrae.fr/wheatis/join
<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /></figure>

# Data exchange format

<table><thead><tr><th>Field</th></tr></thead><tbody><tr><td><ul><li>name</li><li>url</li><li>description</li><li>entryType</li><li>species</li><li>node</li><li>databaseName</li></ul></td></tr></tbody></table>

<table><thead><tr><th>Status</th></tr></thead><tbody><tr><td><ul><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li><li>mandatory</li></ul></td></tr></tbody></table>

<table><thead><tr><th>Cardinality</th></tr></thead><tbody><tr><td><ul><li>1</li><li>1</li><li>1</li><li>1</li><li>1-*</li><li>1</li><li>1</li></ul></td></tr></tbody></table>

<table><thead><tr><th>Constraints</th></tr></thead><tbody><tr><td><ul><li>unique</li><li>none</li><li>none</li><li>cf. list in doc, recom.</li><li>cf. Species list below</li><li>same for all a dataset</li><li>none</li></ul></td></tr></tbody></table>

* WheatIS species list: Aegilops*, Hordeum*, Triticum*, Wheat*

* Format: JSON or TSV, as you wish!

* Web server: HTTP of FTP, as you wish!

* The up-to-date format is always available at https://urgi.versailles.inrae.fr/wheatis/join
# Demo

## Data providers

### INRAE-URGI

IWGSC@GnplS [19,195,264]

GnplS [642,142]

OpenMinTeD@GnplS [1,589]

WheatIS File Repository [6]

### EBI

Ensembl Plants [1,168,762]

### IPK

CR-EST [199,220]

GEBIS [51,302]

MetaCrop [355]

### Gramene

Gramene [229,851]

### T3

The Triticeae Toolbox [206,406]

UniProt by T3 [16,607]

### UWA

Wheat Pangenome [167,167]

### South Green

AgroLD [137,060]

### Rothamsted Research

KnetMiner [108,474]

### GrainGenes

GrainGenes [20,190]

Komugi wheat gene catalog by

GrainGenes [3,119]

### PGSB

CrowsNest [13,324]

### CIMMYT

CIMMYT Publications [1,605]

CIMMYT Datasets [183]

### IPGPAS

PlantPhenoDB [6]

## WheatIS

### Wheat Information System

<figure><img src="image_52.png" /></figure>

Examples: yield, fhb

Search

More... ▼

<figure><img src="image_53.png" /></figure>

About

Join us

Legal mentions

Help
# Demo

## Data providers

### INRAE-URGI

IWGSC@GnplS [19,195,264]

GnplS [642,142]

OpenMinTeD@GnplS [1,589]

WheatIS File Repository [6]

### EBI

Ensembl Plants [1,168,762]

### IPK

CR-EST [199,220]

GEBIS [51,302]

MetaCrop [355]

### Gramene

Gramene [229,851]

### T3

The Triticeae Toolbox [206,406]

UniProt by T3 [16,607]

### UWA

Wheat Pangenome [167,167]

### South Green

AgroLD [137,060]

### Rothamsted Research

KnetMiner [108,474]

### GrainGenes

GrainGenes [20,190]

Komugi wheat gene catalog by GrainGenes [3,119]

### PGSB

CrowsNest [13,324]

### CIMMYT

CIMMYT Publications [1,605]

CIMMYT Datasets [183]

### IPGPAS

PlantPhenoDB [6]

## WheatIS

### Wheat Information System

<figure><img src="image_52.png" /></figure>

Examples: yield, fhb

Search

More... ▼

About

Join us

Legal mentions

Help
<figure><img src="image_54.png" /></figure>

Species

<figure><img src="image_55.png" /></figure>

Triticum [1]

Results 1 to 1 from 1

10.1007/s00122-012-1838-2 - OpenMinTeD@GnpIS

Bibliography

Triticum

Bibliography OpenMinTeD 10.1007/s00122-012-1838-2 Mapping QTL for <span class='openminted_phenotype'>resistance to eyespot of <span class='openminted_taxon'>[...] 415</span>, and <span class='openminted marker'>cfd2</span> are tightly linked to Q.<span class='openminted marker'>cfd2</span> are tightly linked to Q.</td>

Data type

<figure><img src="image_56.png" /></figure>

Bibliography [1]

Connection
((A AND B) OR C))

<figure><img src="image_57.png" /></figure>

Database

<figure><img src="image_58.png" /></figure>

IWGSC@GnpIS [4]

<figure><img src="image_59.png" /></figure>

OpenMinTeD@GnpIS [1]

Data provider

<figure><img src="image_60.png" /></figure>

INRAE-URGI [1]

browse chr4A_7333656_7333940_CFD_SSR_TRIMMED - IWGSC@GnpIS

Gene annotation

Triticum aestivum

SEQUENCE FEATURE IWGSC@GnpISchr4A_7333656_7333940_CFD_SSR_TRIMMED Start = 7333656, End = 7333940, Strand = 0, Source = ePCR, Seq_id = chr4A, Size = 283, Marker = CFD2, Id = CFD2, Type = similarity, Motif = ca(11) Triticum aestivum similarity chr4 ... (Expand)

10.1007/s00122-012-1838-2 - OpenMinTeD@GnpIS

Bibliography

Triticum

Bibliography OpenMinTeD 10.1007/s00122-012-1838-2 Mapping QTL for <span class='openminted_phenotype'>resistance to eyespot of <span class='openminted_taxon'>[...] 415</span>, and <span class='openminted marker'>cfd2</span> are tightly linked to Q.<span class='openminted marker'>cfd2</span> are tightly linked to Q.</td>
<figure><img src="image_53.png" /></figure>

### Species

<figure><img src="image_54.png" /></figure>

Triticum [1]

Results 1 to 1 from 1

10.1007/s00122-012-1838-2 - OpenMinTeD@GnpIS

Bibliography

Triticum

Bibliography OpenMinTeD 10.1007/s00122-012-1838-2 Mapping QTL for <span class='openminted_phenotype'>resistance to eyespot of <span class='openminted_taxon'>[...] 415</span>, and <span class='openminted marker'>cfd2</span> are tightly linked to Q.<span class='openminted marker'>cfd2</span> are tightly linked to Q.</td>

### Data type

<figure><img src="image_55.png" /></figure>

Bibliography [1]

WheatIS
 connection
 (A) (B) (C)

<figure><img src="image_56.png" /></figure>

### Database

<figure><img src="image_57.png" /></figure>

IWGSC@GnpIS [4]

<figure><img src="image_58.png" /></figure>

OpenMinTeD@GnpIS [1]

### Data provider

<figure><img src="image_59.png" /></figure>

INRAE-URGI [1]

browse chr4A_7333656_7333940_CFD_SSR_TRIMMED - IWGSC@GnpIS

Gene annotation

Triticum aestivum

SEQUENCE FEATURE IWGSC@GnpISchr4A_7333656_7333940_CFD_SSR_TRIMMED Start = 7333656, End = 7333940, Strand = 0, Source = ePCR, Seq_id = chr4A, Size = 283, Marker = CFD2, Id = CFD2, Type = similarity, Motif = ca(11) Triticum aestivum similarity chr4 ... (Expand)

10.1007/s00122-012-1838-2 - OpenMinTeD@GnpIS

Bibliography

Triticum

Bibliography OpenMinTeD 10.1007/s00122-012-1838-2 Mapping QTL for <span class='openminted_phenotype'>resistance to eyespot of <span class='openminted_taxon'>[...] 415</span>, and <span class='openminted marker'>cfd2</span> are tightly linked to Q.<span class='openminted marker'>cfd2</span> are tightly linked to Q.</td>
<figure><img src="image_61.png" /></figure>

<figure><img src="image_62.png" /></figure>

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

Gene-based displays

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

Summary

- Splice variants

- Transcript comparison

- Gene alleles

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

Sequence

- Secondary Structure

- Gene families

- Literature

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

Plant Compara

- Genomic alignments

- Gene tree

- Gene gain/loss tree

- Orthologues

- Paralogues

- Homoeologues

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

Pan-taxonomic Compara

- Gene Tree

- Orthologues

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

Ontologies

- GO: Biological process

- GO: Cellular component

- GO: Molecular function

- Phenotypes

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

Genetic Variation

- Variant table

- Variant image

- Structural variants

- Gene expression

- Pathway

- Regulation

- External references

- Supporting evidence

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

ID History

- Gene history

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

Configure this page

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

Custom tracks

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

Export data

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

Share this page

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

Bookmark this page

Ensembl Plants is produced in collaboration with Gramene

Gene: TraesCS2A02G151900

Description

Uncharacterized protein At3g57150 (Fragment) [Source:Projected from Arabidopsis thaliana (AT3G57150) UniProtKB/TrfEMBL;Acc:C0SVF3]

Location

Chromosome 2A: 100.113.981-100.117.432 forward strand.

About this gene

This gene has 1 transcript (splice variant) and 144 orthologues.

Transcripts

Show transcript table

Summary 🔍

Gene type

Protein coding

Annotation method

Genes annotated with high confidence by IWGSC

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

Go to Region in Detail for more tracks and navigation options (e.g. zooming)

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

Drag/Select: ↔

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

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

Configuring the display

Tip: use the "Configure this page" link on the left to show additional data in this region.

Ensembl Plants release 48 - August 2020 © EMBL-EBI

About Us

About us

Contact us

Citing Ensembl Genomes

Get help

Using this website

Documentation

Adding custom tracks

Our sister sites

Ensembl

Ensembl Bacteria

Ensembl Fungi

Follow us

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

Blog

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

Twitter
<figure><img src="image_60.png" /></figure>

<figure><img src="image_61.png" /></figure>

<figure><img src="image_62.png" /></figure>

## Gene-based displays

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

### Summary

- Splice variants

- Transcript comparison

- Gene alleles

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

### Sequence

- Secondary Structure

- Gene families

- Literature

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

### Plant Compara

- Genomic alignments

- Gene tree

- Gene gain/loss tree

- Orthologues

- Paralogues

- Homoeologues

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

### Pan-taxonomic Compara

- Gene Tree

- Orthologues

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

### Ontologies

- GO: Biological process

- GO: Cellular component

- GO: Molecular function

- Phenotypes

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

### Genetic Variation

- Variant table

- Variant image

- Structural variants

- Gene expression

- Pathway

- Regulation

- External references

- Supporting evidence

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

### ID History

- Gene history

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

Configure this page

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

Custom tracks

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

Export data

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

Share this page

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

Bookmark this page

## Gene: TraesCS2A02G151900

### Description

Uncharacterized protein At3g57150 (Fragment) [Source:Projected from Arabidopsis thaliana (AT3G57150) UniProtKB/TrfEMBL;Acc:C0SVF3]

### Location

Chromosome 2A: 100.113.981-100.117.432 forward strand.

### About this gene

This gene has 1 transcript (splice variant) and 144 orthologues.

### Transcripts

Show transcript table

## Summary 🔍

### Gene type

Protein coding

### Annotation method

Genes annotated with high confidence by IWGSC

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

Go to Region in Detail for more tracks and navigation options (e.g. zooming)

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

Drag/Select: ↔

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

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

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

## Configuring the display

Tip: use the "Configure this page" link on the left to show additional data in this region.

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

<figure><img src="image_81.png" /></figure>
<figure><img src="image_82.png" /></figure>

H

TRIUR3_07354 *Triticum urartu*

Putative deoxyribonuclease TATDN1

Model Species Homology

Zm00001d007881 Zea mays

TatD related DNase

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

Login

<figure><img src="image_84.png" /></figure>

New

T3/Wh

## Species

☐ Human

☐ Viral

☐ Triticale

☐ Triticaryo

☐ Brassica

☐ Distort

☐ Aegilops

## Data

☐ Intel

☐ German

☐ Go

☐ Intel

☐ Intel

☐ Go

☐ Intel

## Data

☐ Gram

## Data

Release Notes (62)

About

Contact

Feedback

Privacy

☐ INR

☐ CIN

☑ Gramene

☐ Rot

☐ Gram

☐ T3

☐ South

☐ IPK

☐ IPK

Gramene is a collaborative effort among Cold Spring Harbor Laboratory, Oregon State University, and EMBL-EBI.

Funding is provided by the NSF and USDA ARS.

## Application Info

• Data Release 62

• Gramene Search UI LOCAL DEVELOPMENT BUILD

• Built on January 14th 2020 at 1:01:57 pm

## Actions

Reset Gramene Search
TRIUR3_07354

Triticum urartu

Putative deoxyribonuclease TATDN1

Model Species Homology

Zm00001d007881 Zea mays

TatD related DNase

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

New

T3/Wh

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

Login

## Special

☐ Human

☐ Voluntary

☐ Tritic

☐ Tritic

☐ Bra

☐ dist

☐ Aeg

## Data

☐ Intel

☐ Ger

☐ Go

☐ Intel

☐ Inte

☐ Go

☐ Inte

## Data

☐ Gra

## Data

Release Notes (62)

About

Cite

Feedback

Privacy

☐ INR

☐ CIN

☑ Gra

☐ Rot

☐ Gra

☐ T3

☐ Sou

☐ IPK

☐ IPK

Gramene is a collaborative effort among Cold Spring Harbor Laboratory, Oregon State University, and EMBL-EBI.

Funding is provided by the NSF and USDA ARS.

## Compara Gene Tree

<figure><img src="image_84.png" /></figure>

Gramene

Search for genes, species, pathways, ontology terms, domains...

Gene | TRIUR3_07354

<figure><img src="image_85.png" /></figure>

1 genes in 1 genomes

<figure><img src="image_86.png" /></figure>

<figure><img src="image_87.png" /></figure>

<figure><img src="image_88.png" /></figure>

Search Gramene

Show All Homologs 91

Show Orthologs 89

Links to other resources

Ensembl Gene Tree view

## Application Info

* Data Release 62

* Gramene Search UI LOCAL DEVELOPMENT BUILD

* Built on January 14th 2020 at 1:01:57 pm

## Actions

Reset Gramene Search
New features:
ontology annotation

☐ Link literature with experimental data (genotyping, phenotyping...) using ontology annotation

☐ Corpus of ~1600 wheat open access publications

☐ Text mining ontology: Wheat Trait Ontology
http://wheat.agroportal.lirmm.fr/ontologies/WHEATPHENOTYPE

☐ Semantic facet filtering
New features:
ontology annotation

Link literature with experimental data (genotyping, phenotyping...) using ontology annotation

Corpus of ~1600 wheat open access publications

Text mining ontology: Wheat Trait Ontology
http://wheat.agroportal.lirmm.fr/ontologies/WHEATPHENOTYPE

Semantic facet filtering
New features:
URL derefeencing

All search parameters and filters are available in the
URL for later direct reference, ie.:

https://urgi.versailles.inrae.fr/wheatis/search?query=yield&node=Gramene&entry=Gene&species=Triticum%20urartu
New features:
URL derefeencing

All search parameters and filters are available in the
URL for later direct reference, ie.:

https://urgi.versailles.inrae.fr/wheatis/search?query=yield&node=Gramene&entry=Gene&species=Triticum%20urartu
# New features: synonym enrichment

<figure><img src="image_85.png" /></figure>

Home

WheatIS website

Wheat@URGI

More...

<figure><img src="image_86.png" /></figure>

einkorn wheat

Search

## Species (290)

Filter on Species...

Results 1 to 20 from 197 222 (limited to 10 000)

Marquis*4/2/Stewart*3/Triticum monococcum - GrainGenes

Germplasm

Triticum aestivum

Germplasm GrainGenes Marquis*4/2/Stewart*3/Triticum monococcum L. Unknown Germplasm Type. Marquis*4/2/Stewart*3/Triticum monococcum Triticum aestivum ... (Expand)

## Data type (20)

Filter on Data type...

2006380 - GEBIS

Triticum monococcum L.

2006380 genbank_passport_data GEBIS Triticum monococcum L. ACCESSION NUMBER: TRI 29537; BOTANICAL NAME: Triticum monococcum L.; OTHER NAMES: Albini; ANNUALITY: spring type; SAMPLE STATUS: Advanced/improved cultivar; COUNTRY OF ORIGIN: Germany; ... (Expand)

## Database (17)

Filter on Database...

617 - GEBIS

Triticum monococcum L. var. vulgare Körn

617 genbank_passport_data GEBIS Triticum monococcum L. var. vulgare Körn ACCESSION NUMBER: TRI 617; BOTANICAL NAME: Triticum monococcum L. var. vulgare Körn.; ANNUALITY: spring type; SAMPLE STATUS: Traditional cultivar/landrace; COUNTRY OF ORIGIN: Albania; ... (Expand)

## Data provider

☐ UWA [167 167]

☐ INRAE-URGI [12 224]

☐ GrainGenes [8 008]

☐ IPK [6 706]

☐ CIMMYT [1 696]

☐ T3 [1 353]

☐ Rothamsted Research [63]

☐ Gramene [4]

☐ IPGPAS [1]

2009 - GEBIS

Triticum monococcum L. var. macedonicum papag

2009 genbank_passport_data GEBIS Triticum monococcum L. var. macedonicum Papag ACCESSION NUMBER: TRI 2009; BOTANICAL NAME: Triticum monococcum L. var. macedonicum Papag.; ANNUALITY: spring type; SAMPLE STATUS: Traditional cultivar/landrace; COUNTRY OF ORIG ... (Expand)

644 - GEBIS

Triticum monococcum L. var. vulgare Körn

644 genbank_passport_data GEBIS Triticum monococcum L. var. vulgare Körn ACCESSION NUMBER: TRI 644; BOTANICAL NAME: Triticum monococcum L. var. vulgare Körn.; ANNUALITY: spring type; SAMPLE STATUS: Traditional
# New features: synonym enrichment

<figure><img src="image_89.png" /></figure>

Home

WheatIS website

Wheat@URGI

More...

<figure><img src="image_90.png" /></figure>

einkorn wheat

Search

## Species (290)

Filter on Species...

Results 1 to 20 from 197 222 (limited to 10 000)

Marquis*4/2/Stewart*3/Triticum monococcum - GrainGenes

Germplasm

Triticum aestivum

Germplasm GrainGenes Marquis*4/2/Stewart*3/Triticum monococcum L. Unknown Germplasm Type. Marquis*4/2/Stewart*3/Triticum monococcum L. Triticum aestivum ... (Expand)

## Data type (20)

Filter on Data type...

2006380 - GEBIS

Triticum monococcum L.

2006380 genbank_passport_data GEBIS Triticum monococcum L. ACCESSION NUMBER: TRI 29537; BOTANICAL NAME: Triticum monococcum L.; OTHER NAMES: Albini; ANNUALITY: spring type; SAMPLE STATUS: Advanced/improved cultivar; COUNTRY OF ORIGIN: Germany; ... (Expand)

## Database (17)

Filter on Database...

617 - GEBIS

Triticum monococcum L. var. vulgare Körn

617 genbank_passport_data GEBIS Triticum monococcum L. var. vulgare Körn ACCESSION NUMBER: TRI 617; BOTANICAL NAME: Triticum monococcum L. var. vulgare Körn.; ANNUALITY: spring type; SAMPLE STATUS: Traditional cultivar/landrace; COUNTRY OF ORIGIN: Albania; ... (Expand)

## Data provider

☐ UWA [167 167]

☐ INRAE-URGI [12 224]

☐ GrainGenes [8 008]

☐ IPK [6 706]

☐ CIMMYT [1 696]

☐ T3 [1 353]

☐ Rothamsted Research [63]

☐ Gramene [4]

☐ IPGPAS [1]

2009 - GEBIS

Triticum monococcum L. var. macedonicum papag

2009 genbank_passport_data GEBIS Triticum monococcum L. var. macedonicum Papag ACCESSION NUMBER: TRI 2009; BOTANICAL NAME: Triticum monococcum L. var. macedonicum Papag.; ANNUALITY: spring type; SAMPLE STATUS: Traditional cultivar/landrace; COUNTRY OF ORIG ... (Expand)

644 - GEBIS

Triticum monococcum L. var. vulgare Körn

644 genbank_passport_data GEBIS Triticum monococcum L. var. vulgare Körn ACCESSION NUMBER: TRI 644; BOTANICAL NAME: Triticum monococcum L. var. vulgare Körn.; ANNUALITY: spring type; SAMPLE STATUS: Traditional
New features:
addition of BrAPI sources

<figure><img src="image_87.png" /></figure>
New features:
addition of BrAPI sources

<figure><img src="image_91.png" /></figure>
# How to contribute/join

## How to join the wheat data?

If you want your information system to be referenced, you to contact us as soon as possible so that we can provide you with the best way to go ahead.

Note that since the tool makes a backlink to your information system, we need a URL allowing researchers to get detailed information about the indexed entry directly in your information system.

## Overview of the metadata associated to each searchable entry/document

* a short *name* identifying uniquely the entry, ie. `BTH_Le_Moulon_2000_SetA`

* an *url* linking back to the entry in your own web application, ie. https://urgi.versailles.inrae.fr/ephesis/ephesis/viewer.do#trialCard/trialId=56

* a *description*, of the entry that contains all the relevant keywords allowing to find your entry. All the terms of this field are used by the search tool to allow users to find entries

* an *entryType* describing the type of the entry, that could be any of the terms listed in the dedicated section below

* a *species* field, containing the species related to the entry (zero, one or several, but it is highly recommended to provide at least one)

* a *node*, the name of your laboratory/institute, it should be the same for all the entities you manage

* a *databaseName*, the name of the database from which the entry has been extracted. It can differ from one entry to another if you handle several databases

## Detailed specifications for the metadata fields

### name

<figure><img src="image_88.png" /></figure>

The value of the *name* field must be unique in your own dataset and should be clear enough to help scientists to identify at the first glance this entry among the other.

<table><thead><tr><td>Status</td><td>Cardinality</td><td>Constraints</td></tr></thead><tbody><tr><td>Mandatory</td><td>1</td><td>Unique</td></tr></tbody></table>

<figure><img src="image_89.png" /></figure>
# How to contribute/join

## How to join the wheatIS data?

If you want your information system to be referenced, you to **contact us** as soon as possible so that we can provide you with the best way to go ahead.

Note that since the tool makes a backlink to your information system, we need a URL allowing researchers to get detailed information about the indexed entry directly in your information system.

About

Join us

Terms of use

Help

News/Perspectives

## Overview of the metadata associated to each searchable entry/document

* a short *name* identifying uniquely the entry, ie. `BTH_Le_Moulon_2000_SetA`

* an *url* linking back to the entry in your own web application, ie. https://urgi.versailles.inrae.fr/ephesis/ephesis/viewer.do#trialCard/trialId=56

* a *description*, of the entry that contains all the relevant keywords allowing to find your entry. All the terms of this field are used by the search tool to allow users to find entries

* an *entryType* describing the type of the entry, that could be any of the terms listed in the dedicated section below

* a *species* field, containing the species related to the entry (zero, one or several, but it is highly recommended to provide at least one)

* a *node*, the name of your laboratory/institute, it should be the same for all the entities you manage

* a *databaseName*, the name of the database from which the entry has been extracted. It can differ from one entry to another if you handle several databases

## Detailed specifications for the metadata fields

### name

The value of the *name* field must be unique in your own dataset and should be clear enough to help scientists to identify at the first glance this entry among the other.

<table><thead><tr><td>Status</td><td>Cardinality</td><td>Constraints</td></tr></thead><tbody><tr><td>Mandatory</td><td>1</td><td>Unique</td></tr></tbody></table>
# Perspectives

## Perspectives

2023

**Monitor outgoing traffic towards partner databases**

This metric will trace the impact of the WheatIS data portal, hence promoting its use.

**Display date of last data update**

Make the data loading process smoother and display the date of the last data update in the web interface.

**Long term perspectives**

**Extend ontology annotation**

The 2020 ontology annotation feature is expected to be extended to other kind of documents (any document containing a supported ontology term) as well as using other ontologies (such as Wheat Crop ontology, Plant Ontology, or Wheat Trait and Phenotype Ontology).

**Allow search for exact phrases**

Allow searching group of terms linked together, ie. "fusarium head blight". Currently, any of the 3 terms are searched independently, resulting in a lot of false positives.

**Review the storage of data**

Currently the data is stored next to the code into Git LFS. We plan to review this approach to reduce the storage cost.

**Download results**

Add a download feature allowing to get batch results in a tabulated and/or JSON format. Number of results to be clarified.

**Add Bioschemas.org sources**

Web pages resources marked with Bioschemas.org annotations will be indexed in the frame an ELIXIR infrastructure commissioned service.
# Perspectives

## Perspectives

### 2023

**Monitor outgoing traffic towards partner databases**

This metric will trace the impact of the WheatIS data portal, hence promoting its use.

**Display date of last data update**

Make the data loading process smoother and display the date of the last data update in the web interface.

**Long term perspectives**

**Extend ontology annotation**

The 2020 ontology annotation feature is expected to be extended to other kind of documents (any document containing a supported ontology term) as well as using other ontologies (such as Wheat Crop ontology, Plant Ontology, or Wheat Trait and Phenotype Ontology).

**Allow search for exact phrases**

Allow searching group of terms linked together, ie. "fusarium head blight". Currently, any of the 3 terms are searched independently, resulting in a lot of false positives.

**Review the storage of data**

Currently the data is stored next to the code into Git LFS. We plan to review this approach to reduce the storage cost.

**Download results**

Add a download feature allowing to get batch results in a tabulated and/or JSON format. Number of results to be clarified.

**Add Bioschemas.org sources**

Web pages resources marked with Bioschemas.org annotations will be indexed in the frame an ELIXIR infrastructure commissioned service.
# Beyond WheatIS: other species/communities

* ELIXIR: European Infrastructure for life science

* ELIXIR Plant Data Search Service: FAIDARE

* Data repositories federation - extends WheatIS

* FAIDARE is global, beyond Elixir

<figure><img src="image_90.png" /></figure>

<figure><img src="image_91.png" /></figure>

https://urgi.versailles.inrae.fr/faidare/
# Beyond WheatIS: other species/communities

* ELIXIR: European Infrastructure for life science

* ELIXIR Plant Data Search Service: FAIDARE

* Data repositories federation - extends WheatIS

* FAIDARE is global, beyond Elixir

<figure><img src="image_92.png" /></figure>

<figure><img src="image_93.png" /></figure>

https://urgi.versailles.inrae.fr/faidare/
Examples: yield, fhb

### Species (163)

Filter on Species...

### Taxon group (1,828)

Vitis [5,015,574]×

Filter on Taxon group...

### Data type (12)

Filter on Data type...

### Collection ②

☐ None [5,002,747]

☐ Grapevine BRC [12,827]

☐ CRB-Vigne-Vassal [435]

☐ popMtp3297 (Grenache N x Syrah N) - popMtp3298 (Syrah N x Grenache N) [191]

☐ RlxGW120 [124]

☐ Panel-Assos-279-Montpellier [31]

### Database

☐ GnpIS [4,971,976]

☐ Ensembl Plants [30,661]

☐ brapi@INRAE-URGI [12,881]

☐ brapi@EVA [55]

☐ MetaCrop [1]

### Data provider

☐ INRAE-URGI [4,984,857]

☐ EBI [30,661]

☐ EVA [55]

☐ IPK [1]

Results 1 to 20 of 10,000

All

Germplasm

### BQ794645 - GnpIS

Marker **Vitis vinifera L.**

BQ794645 is a PCR marker from taxon Vitis vinifera L.

### BQ794757 - GnpIS

Marker **Vitis vinifera L.**

BQ794757 is a PCR marker from taxon Vitis vinifera L.

### BQ795963 - GnpIS

Marker **Vitis vinifera L.**

BQ795963 is a PCR marker from taxon Vitis vinifera L.

### BQ797780 - GnpIS

Marker **Vitis vinifera L.**

BQ797780 is a PCR marker from taxon Vitis vinifera L.

### BQ797840 - GnpIS

Marker **Vitis vinifera L.**

BQ797840 is a PCR marker from taxon Vitis vinifera L.

### BQ798928 - GnpIS

Marker **Vitis vinifera L.**

BQ798928 is a PCR marker from taxon Vitis vinifera L.

### BQ798952 - GnpIS

Marker **Vitis vinifera L.**

BQ798952 is a PCR marker from taxon Vitis vinifera L.

### BQ799093 - GnpIS

Marker **Vitis vinifera L.**

BQ799093 is a PCR marker from taxon Vitis vinifera L.

### BQ799904 - GnpIS

Marker **Vitis vinifera L.**

BQ799904 is a PCR marker from taxon Vitis vinifera L.
Examples: yield, fhb

Species (163)

Filter on Species...

Taxon group (1,828)

Vitis [5,015,574]×

Filter on Taxon group...

Data type (12)

Filter on Data type...

Collection ②

☐ None [5,002,747]

☐ Grapevine BRC [12,827]

☐ CRB-Vigne-Vassal [435]

☐ popMtp3297 (Grenache N x Syrah N) - popMtp3298 (Syrah N x Grenache N) [191]

☐ RlxGW120 [124]

☐ Panel-Assos-279-Montpellier [31]

Database

☐ GnpIS [4,971,976]

☐ Ensembl Plants [30,661]

☐ brapi@INRAE-URGI [12,881]

☐ brapi@EVA [55]

☐ MetaCrop [1]

Data provider

☐ INRAE-URGI [4,984,857]

☐ EBI [30,661]

☐ EVA [55]

☐ IPK [1]

Results 1 to 20 of 10,000

All

Germplasm

BQ794645 - GnpIS

Marker Vitis vinifera L.

BQ794645 is a PCR marker from taxon Vitis vinifera L.

BQ794757 - GnpIS

Marker Vitis vinifera L.

BQ794757 is a PCR marker from taxon Vitis vinifera L.

BQ795963 - GnpIS

Marker Vitis vinifera L.

BQ795963 is a PCR marker from taxon Vitis vinifera L.

BQ797780 - GnpIS

Marker Vitis vinifera L.

BQ797780 is a PCR marker from taxon Vitis vinifera L.

BQ797840 - GnpIS

Marker Vitis vinifera L.

BQ797840 is a PCR marker from taxon Vitis vinifera L.

BQ798928 - GnpIS

Marker Vitis vinifera L.

BQ798928 is a PCR marker from taxon Vitis vinifera L.

BQ798952 - GnpIS

Marker Vitis vinifera L.

BQ798952 is a PCR marker from taxon Vitis vinifera L.

BQ799093 - GnpIS

Marker Vitis vinifera L.

BQ799093 is a PCR marker from taxon Vitis vinifera L.

BQ799904 - GnpIS

Marker Vitis vinifera L.

BQ799904 is a PCR marker from taxon Vitis vinifera L.
Acknowledgements

<figure><img src="image_92.png" /></figure>

Raphaël Flores
Cyril Pommier
Maud Marty
Célia Michotey
Erik Kimmel
Nicolas Francillonne
A.F. Adam-Blondon
Hadi Quesneville
Michael Alaux

<figure><img src="image_93.png" /></figure>

<figure><img src="image_94.png" /></figure>

wheatIS

WHEAT INFORMATION SYSTEM

<figure><img src="image_95.png" /></figure>

WheatIS Expert Working Group

<figure><img src="image_96.png" /><figcaption>Mr. Michael Alaux</figcaption></figure>

<figure><img src="image_97.png" /><figcaption>Dr. Ruth Bastow</figcaption></figure>

<figure><img src="image_98.png" /><figcaption>Dr. Ule Baumann</figcaption></figure>

<figure><img src="image_99.png" /><figcaption>Dr. Vijai Bhaduria</figcaption></figure>

<figure><img src="image_100.png" /><figcaption>Dr. Mario Caesùno</figcaption></figure>

<figure><img src="image_101.png" /><figcaption>Dr. Laurel Cooper</figcaption></figure>

<figure><img src="image_102.png" /><figcaption>Dr. Robert Davey</figcaption></figure>

<figure><img src="image_103.png" /><figcaption>Dr. Kate Dreher</figcaption></figure>

<figure><img src="image_104.png" /><figcaption>Prof. Jorge Dubcovsky</figcaption></figure>

<figure><img src="image_105.png" /><figcaption>Dr. Sarah Dyer</figcaption></figure>

<figure><img src="image_106.png" /><figcaption>Prof. David Edwards</figcaption></figure>

<figure><img src="image_107.png" /><figcaption>Dr. Paul Korsuy</figcaption></figure>

<figure><img src="image_108.png" /><figcaption>Prof. Gerard Lezo</figcaption></figure>

<figure><img src="image_109.png" /><figcaption>Prof. David Marshall</figcaption></figure>

<figure><img src="image_110.png" /><figcaption>Dr. Klaus Mayer</figcaption></figure>

<figure><img src="image_111.png" /><figcaption>Dr. Amیدou N'Diye</figcaption></figure>

<figure><img src="image_112.png" /><figcaption>Dr. Hadi Quesneville</figcaption></figure>

<figure><img src="image_113.png" /><figcaption>Prof. Christopher Rawlings</figcaption></figure>

<figure><img src="image_114.png" /><figcaption>Dr. Mark Bewkins</figcaption></figure>

<figure><img src="image_115.png" /><figcaption>Dr. Taker San</figcaption></figure>

<figure><img src="image_116.png" /><figcaption>Prof. Donald Ware</figcaption></figure>

Data providers

<figure><img src="image_117.png" /></figure>

@WheatIS wheatis-contact@wheatis.org

@michaelalaux michael.alaux@inrae.fr
<figure><img src="image_94.png" /></figure>

Raphaël Flores
Cyril Pommier
Maud Marty
Célia Michotey
Erik Kimmel
Nicolas Francillonne
A.F. Adam-Blondon
Hadi Quesneville
Michael Alaux

<figure><img src="image_95.png" /></figure>

# Acknowledgements

<figure><img src="image_96.png" /></figure>

WHEAT
INITIATIVE

<figure><img src="image_97.png" /></figure>

wheatIS
WHEAT INFORMATION SYSTEM

WheatIS Expert Working Group

<figure><img src="image_98.png" /><figcaption>Mr. Michael Alaux</figcaption></figure>

<figure><img src="image_99.png" /><figcaption>Dr. Ruth Bastow</figcaption></figure>

<figure><img src="image_100.png" /><figcaption>Dr. Ulie Baumann</figcaption></figure>

<figure><img src="image_101.png" /><figcaption>Dr. Vijai Bhaduria</figcaption></figure>

<figure><img src="image_102.png" /><figcaption>Dr. Mario Caesùno</figcaption></figure>

<figure><img src="image_103.png" /><figcaption>Dr. Laurel Cooper</figcaption></figure>

<figure><img src="image_104.png" /><figcaption>Dr. Robert Davey</figcaption></figure>

<figure><img src="image_105.png" /><figcaption>Dr. Kate Dreher</figcaption></figure>

<figure><img src="image_106.png" /><figcaption>Prof. Jorge Dubcovsky</figcaption></figure>

<figure><img src="image_107.png" /><figcaption>Dr. Sarah Dyer</figcaption></figure>

<figure><img src="image_108.png" /><figcaption>Prof. David Edwards</figcaption></figure>

<figure><img src="image_109.png" /><figcaption>Dr. Paul Korsley</figcaption></figure>

<figure><img src="image_110.png" /><figcaption>Prof. Gerard Lezo</figcaption></figure>

<figure><img src="image_111.png" /><figcaption>Prof. David Marshall</figcaption></figure>

<figure><img src="image_112.png" /><figcaption>Dr. Klaus Mayer</figcaption></figure>

<figure><img src="image_113.png" /><figcaption>Dr. Amیدou N'Diye</figcaption></figure>

<figure><img src="image_114.png" /><figcaption>Dr. Hadi Quesneville</figcaption></figure>

<figure><img src="image_115.png" /><figcaption>Prof. Christopher Rawlings</figcaption></figure>

<figure><img src="image_116.png" /><figcaption>Dr. Mark Bewkins</figcaption></figure>

<figure><img src="image_117.png" /><figcaption>Dr. Taker San</figcaption></figure>

<figure><img src="image_118.png" /><figcaption>Prof. Donnan Ware</figcaption></figure>

## Data providers

<figure><img src="image_119.png" /></figure>

@WheatIS [wheatis-contact@wheatis.org](mailto:wheatis-contact@wheatis.org)

@michaelalaux [michael.alaux@inrae.fr](mailto:michael.alaux@inrae.fr)