Wheat Data Interoperability charter V3

RDA Candidate Working Group

Wheat Data Interoperability

Case Statement


International context:


Wheat intiative: www.wheatinitiative.org The Wheat Initiative 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.

Main goals :

  • coordinate worldwide research efforts in the fields of wheat genetics, genomics, physiology, breeding and agronomy.

  • provide a forum to facilitate communication between research groups and organisations worldwide.

  • foster communication between the research community, funders and global policy makers at the international level to meet their research and development goals.

  • facilitate and ensure the rapid exchange of information and know-how among researchers, and support knowledge transfer to breeders and farmers

G8+5 open data for agriculture: At the 2013 G-8 Summit (https://sites.google.com/site/g8opendataconference/home), G-8 leaders committed to the New Alliance for Food Security and Nutrition, the next phase of a shared commitment to achieving global food security.

As part of this commitment, they agreed to “share relevant agricultural data available from G-8 countries with African partners and convene an international conference on Open Data for Agriculture, to develop options for the establishment of a global platform to make reliable agricultural and related information available to African farmers, researchers and policymakers, taking into account existing agricultural data systems.”

Working Group Charter


Interoperability is a wide concept that encompasses the ability of organisations to work together towards mutually beneficial and commonly agreed goals. The Working group is using the following definition from the EIF:  ‘An interoperability framework is an agreed approach to interoperability for organisations that wish to work together towards the joint delivery of public services. Within its scope of applicability, it specifies a set of common elements such as vocabulary, concepts, principles, policies, guidelines, recommendations, standards, specifications and practices.’

The working group aims to provide a common framework for describing, representing linking and publishing Wheat data with respect to open standards. Such a framework will promote and sustain Wheat data sharing, reusability and operability. Specifying the Wheat linked data framework will come with many questions: which (minimal) metadata to describe which type of data? Which vocabularies/ontologies/formats? Which good practices?

Mainly based on the the needs of the Wheat initiatiative Information System (WheatIS) in terms of functionalities and data types, the working group will identify relevant use cases in order to produce a  “cookbook” on how to produce “wheat data” that are easily shareable, reusable and interoperable.To do so, the working group will :

  • Run a survey of existing standards and recommendations (vocabularies, ontologies, formats): this survey will identify which standards are adopted in the Wheat data managers community, which ones are missing and which ones can stand as references.

  • Run a survey to identify potential partners willing to share data in order to better understand the players who we will need to actively engage. Identify the main Wheat data types, end-user categories, case studies and provide standards harmonization, guidelines to describe, document, structure and interlink data taking into account the diversity of data types.

  • Evaluate the interest of linked data technologies to improve usage and access to the information.

  • Identify relevant platforms to support the Wheat linked data framework.

Based on a survey report[1] performed in June 2012, the Working group will focus on the following data types, by order of priority: SNP, Genomic annotations, Phenotypes, Genetic Maps, Physical Maps, Germplasm, expression data.

Implementing the framework will help cultivate a Wheat  ecosystem with people familiar with interoperability, organisations ready to collaborate, and common tools and services.

Value proposition

Individuals, communities, and initiatives that will benefit from the Wheat Data Interoperability Guidelines


The Wheat Initiative Information System will be provided with a linked data framework based on community-accepted standards, which ensure data analysis and data integration facilities. Such a framework is a great asset for the Wheat Initiative Information System to provide the analysis functions and other services expected by the researchers.

  • The Wheat data managers and data scientists will have a common and global framework to describe, document, and structure their data.

  • Researchers, growers, breeders, and other data users will have seamless access, use, and reuse to a wide range of Wheat data. Data linking will also ease emergence of new data analyses and knowledge discovery methodologies.

  • Other plants data managers and scientists – will have the benefit of a reusable data framework.

  • Researchers working on other plants will be able to more easily access, reuse and link up Wheat data with their own data.

The “cookbook” might be adapted and adopted for other crops such as rice and maize which are also very important for food security

Key impacts of the RDA Wheat Data Interoperability Guidelines


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

  • Facilitate access, discovery and reuse of Wheat data

  • Facilitate Wheat data integration

Engagement with existing work in the area


The Wheat data interoperability WG is a working group of the RDA Agricultural data interest group.

The working group will take advantage of other RDA’s working group’s production. In particular, the working group will be watchful of working groups concerned with metadata, data harmonization and data publishing.

The working group will also interact with the Wheat Initiative Information System experts and other plant projects such as iPlant Collaborative (http://www.iplantcollaborative.org/),  TransPLANT (http://www.transplantdb.eu/), agINFRA (http://www.aginfra.eu), Plant Ontology (http://www.plantontology.org/), and Crop Ontology (http://www.cropontology.org/).

The Wheat data interoperability group will exploit existing collaboration mechanisms like CIARD (http://www.ciard.net) to get as much as possible stakeholder involvement in the work.

Work plan


  • Form and description of final deliverables

    • A report on the survey of existing standards

    • A Wheat linked data framework specification document (cookbook). The cookbook is intended for the Wheat data managers community, and should provide them with guidelines on what metadata, vocabularies and ontologies they should use to describe, represent and link different types of Wheat data. The cookbook will include a decision tree for describing/representing data based on:

      • data and metadata description recommendations

      • file format recommendations

    • Library of linked vocabularies and ontologies in machine readable formats with respect to the Linked Data standards.

    • A prototype which should be based on an existing Semantic framework such as COEUS (COEUS:http://bioinformatics.ua.pt/coeus/) and should include the set of ontologies recommended in the pre-mentioned cookbook. The goal of the prototype is to propose a ready to use and streamlined framework for:

      • integration of heterogeneous Wheat Data,

      • publishing Wheat Linked Data that facilitate the reuse of the mashed up data by programs and Humans.

  • Months/Deliverables/Milestones

    • Months 1 to 2: Online survey of existing standards and recommendations (vocabularies, ontologies, existing types and formats of wheat research data). Plus identification of end-user categories and relevant platforms.

    • Months 3 to 7: Identification of a set of minimal metadata for each data type and discussions on how to move from a set of unrelated ontologies and vocabularies to a Linked Data framework.

    • Months 8 to 10: First version of the Wheat linked data framework specification document (cookbook).

    • Months 8 to 11: Prototyping - Configuration of an existing Semantic framework with selected ontologies + documentation for selected Wheat Data integration use cases through the prototype.

    • Months 12 to 14: Evaluation of the first version of the cookbook and the prototype by the adoption groups.

    • Months 15 to 16: Final version of the Wheat linked data framework specification (cookbook) + update of the COEUS prototype.

    • Months 15 to 18: Promotion: workshops in connexion with an RDA meeting and the Wheat Initiative events + webinars.

Adoption plan


Our adoption strategy relies on a  network of Adoption Groups. The Adoption Groups will be part of the work process. Indeed, we will survey the Adoption Groups to find out existing standards and practices, and identify gaps that need to be filled. The Adoption Groups will also test the first version of the Wheat linked data framework and give feedback. Finally, the Adoption Groups will endorse the final Wheat linked data framework.

Confirmed Adoption Groups

  • The Wheat Initiative Information System Experts Group: one of the Wheat Initiative objectives is to build an international and  integrated Wheat Information System (WheatIS) intended to an international Wheat community (researchers, growers, breeders, etc.). The WheatIS could operate as a hub and integrate wheat data produced by the community. The working group will base a large part of its specification requirements on the Wheat initiative’s data exchange needs. The Wheat linked data framework will be tested first through the WheatIS. The working group will rely both on the Wheat Initiative members (public research organizations and private companies)  and its community to ensure a large circulation of the Wheat linked data framework and facilitate its adoption.

  • Achieving food security for all is at the heart of FAO's efforts – to make sure people have regular access to enough high-quality food to lead active, healthy lives. FAO’s mandate is to improve nutrition, increase agricultural productivity, raise the standard of living in rural populations and contribute to global economic growth. One of FAO’s principal means to achieve this goal is collecting, disseminating and brokering knowledge.  Therefore FAO has a prime interest on excellent information systems. The  “AIMS team” (Agricultural Information Management Standards; http://aims.fao.org/)  in FAO is engaged in helping to set standards and methodologies for easier sharing and exchange of Agricultural information

  • The International Maize and Wheat Improvement Center (CIMMYT; http://www.cimmyt.org/en/) is the world’s premier center for research, development, and training in maize and wheat and in farming systems for those two essential food crops. From its headquarters in Mexico and offices throughout the developing world, the center works with partners worldwide to reduce poverty and hunger by sustainably increasing the productivity of maize and wheat cropping systems. CIMMYT maintains one of the world’s largest and most diverse maize and wheat seed collections and is best known for work leading to the Green Revolution—the widespread adoption of improved crop varieties and farming practices that saved millions of lives across Asia and for which CIMMYT’s Dr. Norman Borlaug was awarded the 1970 Nobel Peace Prize. CIMMYT is a member of the CGIAR Consortium and receives support from national governments, foundations, development banks, and other public and private agencies.

  • The International Wheat Genome Sequencing Consortium (IWGSC; http://www.wheatgenome.org/) was established by a group of plant scientists, breeders, and growers dedicated to sequencing the wheat genome to enhance our knowledge of the structure and function of the wheat genome. By gaining increased understanding of the biology of agronomically important traits and deploying state-of-the-art molecular tools, plant scientists and breeders will be able to accelerate wheat improvement to meet the challenges of the 21st century. The Consortium is committed to ensuring that the sequence of the wheat genome and the resulting DNA-based tools are available for all to use without restriction.

  • Plant Ontology (http://www.plantontology.org/)

Prospective Adoption Groups

Roles and responsibilities of the adoption groups  

  • The work group will survey the adoption groups, in order to identify and take into account their current practices in terms of data management.

  • The adoption groups will test the first version of the cookbook and their feedback will be considered in the final version.

  • The adoption groups should endorse the best practices and standards promoted in the cookbook.

Initial proposed membership


Esther DZALE YEUMO KABORE, Institut National de la Recherche Agronomique (INRA), Chair

Richard FULSS, International Maize and Wheat Improvement Center (CIMMYT), Chair

Johannes KEIZER, Food and Agriculture Organization (FAO)

Devika MADALLI, Indian Statistical Institute (ISI)

Odile HOLOGNE, Institut National de la Recherche Agronomique (INRA)

Nikos MANOUSELIS, Agro-Know Technologies

Alex WHAN, Commonwealth Scientific and Industrial Research Organisation (CSIRO)

Michael ALAUX, Institut National de la Recherche Agronomique (INRA), also member of the Wheat Initiative Experts Working Group

Cyril POMMIER, Institut National de la Recherche Agronomique (INRA), also member of the transPLANT project

Sophie AUBIN, Institut National de la Recherche Agronomique (INRA)

Helmuth KNUEPFFER, Genbankdokumentation Gatersleben

Hillary CHEN, US office of Science and Technology

Laurel Cooper, Plant Ontology Project

Ruth Bastow, Global Plant Council

Achieving consensus, addressing conflicts, and staying on task and within scope


○   Consensus will be reached via open discussion, voting, and majority considerations informed by evidence where possible.

○   Conflict will first be addressed by WG leaders.  An escalation procedure will be drafted, for example the RDA Council will be consulted, and an independent person not in the WG will be brought in to mediate the conflict.

○   Staying on task and within scope:  we have considerable experience in projects and standards development. The key mechanism for reaching consensus will be through examining evidence and identifying limitations of applicability of competing ideas. In addition, of course, we will agree on a detailed schedule and track action items.

Operation parameters


The work is voluntary, and not every WG member will be able to contribute equally therefore we will aim to fit the work to focus efforts on members’ specific interests but also to ensure that all members can contribute to internal reviews. The WG hold internal assessments every 6 months to ensure the progress of the WG and the timely delivery of outcomes.

WG Assessment


The 6 monthly assessments will involve work group members and also external reviewers who have expertise in this area, including those who declined membership of the working group because of pressure of other work.


Wheat initiative Information System:



GARNet report - Making data accessible to all:


Various relevant refs: