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A gateway between imaging data management tools to enforce FAIR principles – OpenLink

Submission summary

Since 2018, the Institute of Genetics and Molecular and Cell Biology (IGBMC) has been committed to adopt a new approach to drive global changes in scientific data management and follow FAIR principles (Findable, Accessible, Interoperable, Reusable). To meet this challenge, the IGBMC relies on digital tools set up at the national level like OPIDoR data management plan dashboard or the LabGuru electronic laboratory notebook, but also local data management solution like OMERO storage, visualization and annotation tools and an institutional data warehouse that enable researchers to archive their work in a sustainable and secure manner.
To date, we have identified two major parameters that limit the effectiveness of our organization. First, heterogeneous digital tools made available to research teams cause a scattering of data and loss of metadata. Second, beyond the support that can be offered to researchers to use these tools, their adoption or daily use remains complex because it requires a constant and diligent follow-up to keep in track with the FAIR principles.
In this context, the IGBMC aims to associate its IT department, its imaging center and three research teams to carry out an experiment dedicated to the development of 1) a central and transversal gateway tool for the functional integration of the existing data management tools and 2) a methodology for monitoring projects and their data.
The gateway tool, in the form of a web application, will facilitate the transversal identification of projects and their associated data, from the data management plan created on OPIdoR, to the publication, through the LabGuru electronic lab notebook and data processing tools such as OMERO. The aim is to streamline the transfer of data from production to archiving, while automatically enriching metadata. This tool will automate the publication of the archived data in official catalogs and reference them in indexes such as datacite ( for sharing the research outputs. Keeping track of metadata for each dataset is an essential aspect to be compliant with FAIR principles.
In parallel, the development of a methodology for monitoring projects will aim to support the research teams to show them the benefits of developing a data management plan from the beginning of a project, raise awareness of data storage management costs and train them in the FAIR principles.
This experimentation will be carried out on light microscopy image data before extending it to all types of biology data (omics, phenotyping, etc.) for the next stage of the project.
All connectors and gateways as well as dashboards will be designed to be usable in any research lab and released in standard package format under an OpenSource license.

Project coordination

Julien Seiler (Institut de génétique et de biologie moléculaire et cellulaire (UM 41 - UMR 7104 - UMR_S 1258))

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


IGBMC Institut de génétique et de biologie moléculaire et cellulaire (UM 41 - UMR 7104 - UMR_S 1258)

Help of the ANR 93,420 euros
Beginning and duration of the scientific project: January 2020 - 24 Months

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