2026/06/16 by Claire Rioualen, Aurélien Barre, Vincent J. Carey +7 · 1 voice
Biochemistry, Genetics and Molecular Biology · Computer Science · Decision Sciences · #Cell Image Analysis Techniques #Research Data Management Practices #Scientific Computing and Data Management
paper · doi:10.7490/f1000research.1120602.1
openalex publication_date 2026/06/16 · openalex created_date 2026/06/24 · openalex updated_date 2026/07/22
<ns5:p> <ns5:bold>Background.</ns5:bold> Organised yearly since 2018, the ELIXIR BioHackathon brings together scientists from very diverse backgrounds and expertise, to work on innovative projects in a dynamic environment. Beyond the scientific context, it fosters a very social environment, where informal interactions and networking are facilitated. This flagship event is a great illustration of ELIXIR’s 2024-2028 4-tier programme, as well as its core human values: openness, joint efforts, respect and trust. <ns5:bold> </ns5:bold> </ns5:p> <ns5:p/> <ns5:p> <ns5:bold>Science.</ns5:bold> Back at the 2023 BioHackathon, a casual conversation gave birth to a fruitful collaboration between the Bioconductor community and the EDAM group, which is active to this day. About 2,000 Bioconductor software packages have historically been annotated with the biocViews vocabulary, which mostly consists of what we call “topics”. In order to further improve their FAIRness, we decided to use EDAM for their annotation, including “operations” and “data” concepts. </ns5:p> <ns5:p> <ns5:bold> </ns5:bold> </ns5:p> <ns5:p> <ns5:bold>Nodes.</ns5:bold> At the 2024 BioHackathon, our project contributed greatly to advancing this goal, by allowing collaborators from diverse Nodes, backgrounds and locations to participate on-site and remotely. As a result, the biocViews vocabulary was mapped to EDAM concepts, and Bioconductor packages’ metadata were gradually synchronised with the ELIXIR Research Software Ecosystem and the bio.tools registry. </ns5:p> <ns5:p/> <ns5:p> <ns5:bold>Technology.</ns5:bold> At the 2025 BioHackathon, our project focused on the development of EDAM MCP, an MCP server to improve and facilitate the annotation of bioinformatics software by combining several LLM agents and data resources. It also fostered a collaboration with the ELIXIR Metabolomics Community, by using curated metabolomics-related resources as a use case for the benchmarking and evaluation of the results. This evaluation showed significantly better performance over the baseline LLM. </ns5:p> <ns5:p/> <ns5:p> <ns5:bold>People.</ns5:bold> At the core of this project is a fundamental human component. Stemming from an informal interaction, it federated a very diverse working group over the span of two years, going beyond ELIXIR and Europe. Through casual interactions and extra-meetings held at the last European Bioconductor conference in Barcelona (2025), we were able to onboard more people from the community, strengthening the bridge between the Bioconductor and ELIXIR communities. </ns5:p>