# Data stewardship strategy of the Ferments du Futur grand challenge

Erwan Le Floch, Agnès Barnabé, Jonathan Duperrier, Thomas Lacroix, Aaron Millan-oropeza, Jonathan Mineau-Cesari, Mariène Wan, Sophie Schbath, Valentin Loux

► To cite this version:

Erwan Le Floch, Agnès Barnabé, Jonathan Duperrier, Thomas Lacroix, Aaron Millan-oropeza, et al. Data stewardship strategy of the Ferments du Futur grand challenge. Journées Ouvertes Biologie, Informatique, Mathématiques 2025, Jul 2025, Bordeaux, France. 2025. hal-05149332v2

HAL Id: hal-05149332

https://hal.inrae.fr/hal-05149332v2

Submitted on 11 Jul 2025

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_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_2.png" /></figure>

MaiAGE

misole

Erwan LE FLOCH¹,²,³, Agnès BARNABE¹,²,³, Jonathan DUPERRIER¹,²,³, Thomas LACROIX¹, Aaron MILLAN-OROPEZA⁴, Jonathan MINEAU-CESARI⁵,⁶, Mariène WAN⁷, Sophie SCHBATH¹,² and Valentin LOUX¹,²

1 Université Paris-Saclay, INRAE, MaiAGE, 78350, Jouy-en-Josas, France
2 INRAE, BioinfOmics, MIGALE bioinformatics facility, 78350, Jouy-en-Josas, France
3 Ferments du Futur (US INRAE 1503), Orsay, France
4 Université Paris-Saclay, CNRS, INRIA, CentraleSupélec, LISN, 91405, Orsay, France
5 INRAE, DipSO INRAE
6 Université de Montpellier, INRAE, Montpellier SupAgro, SPO, 34080 Montpellier, France
7 INRAE, BioinfOmics, URGI, 78000, Versailles, France

# Data stewardship strategy of the Ferments du Futur grand challenge

The grand challenge **Ferments du Futur** (FdF) was launched in 2022 as a public-private partnership co-led by INRAE and ANIA, with a 48,3 M € funding from the France 2030 investment plan. Every year since then, academic and industrial projects are selected and last 2 years each. These projects use facilities distributed across 7 INRAE research units and an innovation lab, with expertise ranging from food product prototyping to bioinformatics, microbial ecology, biochemical characterization, bio-processes design and host-microorganism interactions.

Data has a central role in FdF. Indeed, one of the goal of FdF is to shift from empirical to data and knowledge driven design of fermented foods. Massive and heterogeneous data are expected to be generated by the various academic and industrial projects. To tackle this data management challenge, the OpenSILEX¹ information system was chosen for its ontology-driven nature, which aligns well with the FAIR data objectives of FdF. **Siduri** is the OpenSILEX implementation developed and hosted at the Migale bioinformatics facility to provide data science services.

However, not only technical but also organizational solutions are needed. A comprehensive **data stewardship** agenda has therefore been designed to support the numerous FdF projects along the data life cycle. The Data Management Plan (DMP) that each project must write and maintain is used as a basis for discussions between the FdF projects and the Siduri team. A two-step training workshop consisting in a webinar followed by a "data party" is organized each year, and results in a "map" of the data expected to be produced in each project. This has an educative goal, but also helps to make sure the upcoming experimental data will fit in the data model behind Siduri.

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

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

## RDM training and support

* FAIR awareness webinars

* Datathons & data mapping

* Online training with OSCAR

* DMP used as a tool

## ... at scale

* For 6 new academic projects every year, for 10 years !

* Each of them having highly heterogeneous data

## Data mapping

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

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

## Siduri data model

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

## Research products categories

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

## Conclusion & Perspectives

* Siduri is a FAIR-by-design information system, that aims to be a reference knowledge base for fermented food experiments.

* Besides technical solutions, data management training and support are leveraged to ensure a smooth adoption of Siduri by the whole Ferments du Futur consortium and beyond.

* Siduri is also an opportunity to contribute evolutions to ontologies such as TransformON², and to define best practices and

data management guidelines for the bioprocesses, fermented foods and microbiome communities.

## References

1. Neveu P. et al. Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. New Phytologist 2019. https://doi.org/10.1111/nph.15385

2. Weber M. et al. PO2/TransformON, an ontology for data integration on food, feed, bioproducts and biowaste engineering. npj Sci Food 2023. https://doi.org/10.1038/s41538-023-00221-2

## Acknowledgments

This work benefited from French government funding managed by the Agence Nationale de la Recherche as part of France 2030 under the reference ANR-22-GDFF-0001.

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

www.fermentsdufutur.eu

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

siduri.migale.inrae.fr