Towards an Integrated
Wheat Information System
- Funding scenarios -
Mario Caccamo & Hadi Quesneville
Contributors : Takeshi Itoh, Paul Kersey, David
Marshall, Cesar Martinez, Dave Matthews, Klaus Mayer,
Franck Röber, Doreen Ware.
WheatIS Expert Working Group
Wheat Initiative steering
board commissioned a
• Build projects
• Build infrastructure
• Report to the
Provide the wheat research community with a single entry
point of access to genetic and genomics resources.
Promote the development of services on top of
current wheat / Triticeae databases.
Authority to define guidelines for data curation,
nomenclature, standards and integration.
Registry for bioinformatics tools.
Build collectively to
better cope with
the needs of the
• Federated Network of Platform
• Ensure each platform sustainability through
promoting their visibility and adoption.
• WheatIS will not replace the current wheat
rapidly build an
• Evolving infrastructure
• Rely on a distributed system.
• Use of Virtual Machine and Cloud
Computing technologies to share easily data and
• WheatIS to support the adoption of standards
and the integration of data
• Gene nomenclature
• Best-practice guidelines
WP5: User interfaces,
outreach, training and
WP1: Central data file
WP2: Distributed index
WP3: Data standards, data
management, and data
WP4: Data and Information
WP6: Coordination and
Implementation: an iterative process
Step1 : Network building
Definition of standards
• define standards, nomenclature, formats,
• meta-data exchange
A web platform to
Step2 : Integrated portal (virtual)
Search of data
• DBs federation
• Google-like search
A portal to access a
network of DBs
Step3 : Integrated DB
Integration of data
• In one place
• Focused on relevant data sets
• Consolidated and consistent
(Previous steps will provide a broad
view of available data)
An integrated DB
ICC & SC feedbacks on EWG plan
ICC & SC
Solutions available in a WheatIS node is
distributed to the other partners
Transparent for the end-users.
Necessitate the adoption by all
platforms of solutions provided by
Facilitate other WheatIS nodes (not yet
identified) to join the initiative.
• Contributions of the partner WheatIS nodes
• Funding institutions dedicating resources to the
• Additional resources will be looked for, from
national or international calls for proposals
• WP3, 5 and 6 could start with
no additional resources.
• WP1, 2 and 4 will require newly
- Scenario 1 -
Additional staff recruited
in 2 leading WheatIS nodes in 2013
• TGAC (BBSRC, UK) and URGI (INRA, France) have already
‣ Distributed storage will be proposed between TGAC and URGI infrastructures.
‣ Funds available in May 2013, first WheatIS delivery for summer 2014.
‣ Quick start
‣ People used to collaborate
‣ Small community consultation
‣ Risk of lack of adoption
‣ One expert informatics engineer for TGAC and one for INRA for one year each.
Approximately 100,000 euros in addition to existing staff salaries.
- Scenario 2 -
Additional funds available immediately in
• Group of WheatIS nodes
‣ Project could start from a collectively chosen solution.
‣ Funds available in May 2013, delivery of a first WheatIS in winter 2014.
‣ Larger collaborative work
‣ Better adoption by the WheatIS nodes
‣ Start is delayed from 6 months
‣ Probably at least one expert informatics engineer per node involved.
Approximately 50,000 euros per nodes for one year, in addition to
existing staff salaries.
- Scenario 3 -
No additional funds available
• Inventory all the partners willing to participate as a
‣ Several projects will be written, coordinated and submitted independently
to fund specific tasks of the projects
‣ The start of the project would depend on the success of the calls for
‣ Large collaborative network,
‣ Almost in its final configuration.
‣ No initial additional funds requested to the institutions.
‣ Best adoption configuration
‣ Start is delayed from at least 1 year
Additional salaries € Meetings Total €
Scenario 1 100,000 50,000 150,000
Scenario 2 50,000
x (wheatIS nodes involved
from the start)
+ (50,000 x nodes)
Scenario 3 0 50,000 50,000
• Organize the first annual meeting in 2013.
• Write a report describing the planned activities.
• Submit a research proposal to get funds for the
implementation of the WheatIS
Catherine Feuillet - INRA - France
Cesar Martinez - CIMMYT - International"
Dave Edwards - University of Queensland - Australia"
David Marshall - James Hutton Institute - UK"
Doreen Ware - Gramene - USA"
Eva Huala - TAIR - USA"
Hirokazu Handa - NIAS - Japan"
Jizeng Jia - CAAS - China"
Jorge Dubcovsky - UC Davis – USA"
Keith Edwards - University of Bristol – UK"
Klaus Mayer - MIPS – Germany"
Paul Kersey - EBI EMBL - International"
Peter Langridge - University of Adelaide - Australia
• Hélène Lucas (INRA)"
• Amanda Collis and Michael Ball (BBSRC)