2026 Groningen Semantic Metabolomics ELIXIR Workshop

Welcome to the official repository for the 2026 Groningen Semantic Metabolomics Workshop (ELIXIR RCI-M). All workshop materials, resources, and session notes will be shared here.

Workshop Overview

Join us at the next ELIXIR RCI-M Metabolomics Workshop, which will be held in person on 16 and 17 February 2026 in the beautiful city of Groningen (NL) — a unique opportunity for the metabolomics community to shape reproducible, comparable, integrable and FAIR metabolomics data!

This event presents the first results of the ELIXIR RCI-M implementation study, which addresses issues of data harmonisation, semantic modelling and metadata standards for metabolomics. Together, we propose to explore new frameworks for integrating our metabolomic profiles across all omics, enriching our annotations and contributing to the development of ontologies necessary for our field, thereby improving comparisons between studies and reliable data interpretation.

Participants will take part in hands-on sessions and learn how to leverage tools (EBI MetaboLights), formats (mzQC, mzTab-M) and semantic resources (Ontologies, OLS). Whether you are a researcher, developer, or data manager, you will have the opportunity to contribute to the next generation of interoperable standards and artefacts, and see how to adopt and evolve them in practice.

Date: 16-17th February 2026
Location: House of Connection - Groningen, Netherlands

More information on the Agenda.

Organisers

Monica Chagoyen - Systems biomedicine lab, Cajal Neuroscience Center, CSIC - ELIXIR-ES
Franck Giacomoni - INRAE - MetaboHUB - ELIXIR-FR
Helge Hecht - RECETOX, Masaryk University - ELIXIR-CZ & EIRENE-CZ
Nils Hoffmann - IBG-5, Forschungszentrum Jülich GmbH - ELIXIR-DE
Peter Horvatovich - University of Groningen - ELIXIR-NL
Steffen Neumann - IPB Halle - ELIXIR-DE
Sanjay Srikakulam - IBG-5, Forschungszentrum Jülich GmbH - ELIXIR-DE
Noemi Tejera Hernandez - European Bioinformatics Institute
Thomas Payne - European Bioinformatics Institute
Elliott James Price - RECETOX, Masaryk University - ELIXIR-CZ & EIRENE-CZ
Magalie Weber - INRAE - DIPSO - MetaboHUB - ELIXIR-FR
Egon Willighagen - Translational Genomics, NUTRIM, Maastricht University - ELIXIR-NL

Agenda

Program Monday, February 16, 2026

09:00-09:10 Opening - Peter Horvatovich
09:10-10:00 Keynote I - Egon Willighagen - WikiPathways: semantic integration of multiomics data doi:10.5281/zenodo.18654362
10:00-11:00 Session I - Facilitating data interpretation and meta-analysis/integration in Metabolomics - Monica Chagoyen, Steffen Neumann, Franck Giacomoni, Magalie Weber
- “Turning Metabolomics Data into Biological Insight: Reporting and Sample Description Matter” + The BioSample description task - 30 min - Monica Chagoyen, Franck Giacomoni
- “Making your results count: best practices in metabolomics reporting” - 30 min - Steffen Neumann
11:00-11:30 Coffee break
11:30-13:00 Hands-on session I - metabolomics (bio)sample description and metabolites results - Monica Chagoyen, Steffen Neumann, Franck Giacomoni, Magalie Weber
- Instructions
- Materials: Participants bring the title page of the paper of their study
- Session: Participant add post-it’s with annotation (including ontology annotation accession!) around it.
- Q&A - 15 min - All
13:00-14:00 Lunch
14:00-15:30 Session II - Semantic Metabolomics Data Model for standardization: Current State Overview - Thomas Payne, Noemi Tejera Hernandez, Franck Giacomoni, Magalie Weber
- Team introduces related RCI-M project milestones and deliverables, including data sharing (landscape with MetaboLights) - 10 min - Thomas Payne
- Data models - Introduction to ISA (original), ISA-API, … - 20 min - Philippe Rocca-Serra
- Ontologies - Introduction - 20 min - Magalie Weber
  - What are ontologies
  - Why ontologies are needed
  - Which tools are useful to search for ontologies and map free text to ontology terms.
  - Which ontologies are relevant.
  - Whether and how to improve existing ontologies.
- Team presents results from efforts to improve current state - 30 min - Thomas Payne
  - Examples
  - Data models - ISA (extended)
  - Ontologies - sources (PSI MS CV, EDAM, ChEBI) - extensions
15:30-16:00 Coffee break
16:00-17:30 Hands-on session II - MetaboLights Study Semantic Curation
- Part 01 - 45 min - Noemi Tejera, Thomas Payne
  - Brief introduction to MetaboLights (+ hands-on exercise)
  - Mapping to ISA - Populate Investigation file in MetaboLights
  - Tasks: Use Publications / results from Hands-on session I (or ‘Example Studies’) to map the identified terms from the morning session into the different sections of a MetaboLights study (Samples, Assays, Metabolites results) - Document
- Part 2 - 30 min - Magalie Weber, Franck Giacomoni
  - Instructions
  - Practical work involving improving or producing annotations.
    - Brief introduction to hands on exercise on Ontologies
    - Identify which ontologies can be used to map terms from the Hands-on sessions I & II outputs
    - Identify ontology gaps and missing information
    - Generate potential roadmap on how to submit those terms to those ontologies
17:30-18:00: Visit Peter Horvatovich’s Analytical Biochemistry laboratory - Groningen
19:00 Dinner: Restaurant WEEVA, Gedempte Zuiderdiep 8-10, 9711 HG Groningen

Program Tuesday, February 17, 2026

09:00-11:00 Hands-on session III - mzQC tutorial - Helge Hecht, Elliott Price, Nils Hoffmann
- Introduction QA/QC - Analytics Perspective - 30 min - Elliott Price
- Interactive Q&A - 15 min - Elliott Price, Nils Hoffmann
- Overview of mzQC - 15 min - Nils Hoffmann
- Overview of msQuality - 45 min - Helge Hecht
- Q&A - 15 min - All
11:00-11:30 Coffee break
11:30-13:00 Session III - Quality Control (QC) and Enhanced Metadata – updates on mzTab-M, mzQC and other standards - Helge Hecht, Nils Hoffmann
- Enabling semantic data integration with enhanced metadata - 5 min - Nils Hoffmann
- Metadata for your tool - hands-on with bio.tools & EDAM - 30 min - Helge Hecht
- QC and reporting survey hands
- Survey QC practices - first results - 15 min - Nils Hoffmann
- What is possible with mzTab-M? Interoperability Hackathon - 15 min - Helge Hecht, Nils Hoffmann
- mzTab-M planned updates (chromatography and methods, study variables) - 15 min - Nils Hoffmann
13:00-14:00 Lunch
14:00-14:45 Keynote II - Lindsey Anderson & Tim van den Bossche (RDA MOMSI Working Group) - The RDA MOMSI Landscape Dashboard: A Tool for Mapping Multi-Omics Standards
14:45-15:30 Panel discussion
15:30-16:00 Wrap-up with feedback to the whole group
- Discuss MSIO and other initiatives
- Standards to consider (e.g., LMRC)
- Overview of other initiatives that aim to improve the current state:
  - Examples: FAIRly, MetabolomicsHub, MOMSI
  - Opportunities for synergies or collaborations
- Future Directions - Next steps toward FAIR data, including Linked (Opened) data, Improved search, Better interoperability

Resources

Elixir community Groningen workshop repository

Groningen workshop shared google drive

📣 Presentations

Opening Session Peter Horvatovich - Presentation
Keynote: Egon Willighagen doi:10.5281/zenodo.18654362
Keynote: Tim van den Bossche (VIB, Ugent), Lindsey Anderson (PNLL) Presentation

🛠️ Hands-on Activities

Hands-on I - Metabolomics Biosample Description - Franck Giacomoni, Magalie Weber
Hands-on II - MetaboLights Study Semantic Curation - Noemi Tejera Hernandez, Magalie Weber
Hands-on III - MzQC - Helge Hecht, Elliott Price, Nils Hoffmann

💬 Panel Discussion

Panel Discussion
Q&A Summary

✅ Wrap-up & Outcomes

Workshop Wrap-up
Future Directions & Community Feedback

Groningen Meeting Report

report will be published as possible

How to Use This Repository

Browse the folders above for session materials and documentation.
Download any workshop resource directly from GitHub.
Use the Issues tab for questions or to provide feedback on the event or materials.

Contributing

Contributions are welcome!
You may submit improvements, corrections to documentation, or share additional resources by opening a pull request or issue.

Contact

For inquiries or support, open an Issue or reach out to the workshop organisers:

Main contact: elixir_rci-m_members@groupes.renater.fr
Community website: ELIXIR Metabolomics Community
Project website: Next level of reproducible, comparable and integrable Metabolomics Project

Thank you for participating and contributing to the advancement of semantic-driven metabolomics!