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Tools and methods for extended plant PHENotyping and EnviroTyping services of European Research Infrastructures


Project Coordinated by INRAE (France)

Europe urgently needs to find pathways towards agroecological transition of agroecosystems in support to food security, climate change resilience, biodiversity and soil carbon stocks restoration. In PHENET, the European Research Infrastructures (RI) on plant phenotyping (EMPHASIS), ecosystems experimentation (AnaEE), long-term observation (eLTER) and data management and bioinformatics (ELIXIR) will join their forces to co-develop, with a diversity of innovative companies, new tools and methods – meant to contribute to new RI services – for the identification of future-proofed combinations of species, genotypes and management practices in front of the most likely climatic scenarios across Europe. Ambitioning to go beyond current highly instrumented but often spatially and temporally limited RI installations, PHENET derived services will allow wide access to enlarged sources of in-situ phenotypic and environmental data thanks to (i) new AI-based multi (agroecology-related) traits multi-sensors devices (ii) to unleashed access to high resolution Earth Observation data connected to ground based data, (iii) FAIR data support for connection with (iv) new generation of predictive modeling solutions encompassing AI and digital twins. Developments will be challenged by and implemented in a series of eight Use Cases covering a large range of agroecosystems but also of ecosystems to demonstrate portability of solutions. Several of these Use Cases will mobilize on-farm data. A large effort will be devoted to training RI staff and beyond through a sustained collection of training material fed by experts. Outreaching activities will aim at enlarging the range of RI users. PHENET will not only strengthen RI but will also have major impact on the development of innovative companies on phenotyping, envirotyping and precision agriculture as well as on the emergence of climate smart crop varieties and innovative practices fitted to climate change and agroecological transition.

Funding Source
project budget
10 000 000 EUR
egi budget
90 000 EUR
Contract No.
type of project
Research and innovation
Target Group
Research communities

EGI Foundation role in the project:

Methodology – E-infrastructure services for PHENET

PHENET WP2 will co-design and deploy AI-driven models on the edge resources operated within the experimentation networks. These models will be piloted on a two-tier e-infrastructure: The first tier will be the in-house compute and storage resources operated at the project consortium member institutes. These resources are suitable for functional and small scale validation scenarios. The second tier will be reached by PHENET through the EGI Foundation, coordinator of the pan-European EGI federation. The EGI federation already includes 27 computational clouds to provide resources for international research infrastructures and projects directly. The EGI federation also delivers the Compute Platform of the European Open Science Cloud. EMPHASIS is already using EGI resources from CZ (CESNET), FR (IN2P3) and PL (CYFRONET) (See the EGI-EMPHASIS SLA at EGI Foundation will expand this allocation for PHENET with additional capacities based on project technical requirements, the national footprint of PHENET RIs during project execution time, and the availability to national funding within EGI member states to support crops and ecosystem research. The EGI resource allocation approach will bring the national EGI members and national EMPHASIS, AnaEE and eLTER communities together, aligning national e-infrastructure and research infrastructure funding, ensuring sustainable compute setups for beyond the project. The second tier of the PHENET e-infrastructure will be suitable for scale-out and be able to train and operate large models on big data sets.

T4.1  (the task where EGI is involved)

We had challenges uploading, processing and managing the (literally) millions of files produced by the different  imaging systems. We will explore distributed storage approaches (iRODS – Wageningen) to enable managing large scale research data sets and link these solutions with existing information systems (PHIS) and analysis portals. The primary computing and storage infrastructure will be provided by the consortium members. EGI will bring additional capacities and compute services for the project from its national e-infrastructures, according to to national research and e-infrastructure funding priorities. EGI will also establish liaison between PHENET and relevant services of the European Open Science Cloud.

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