In April, researchers from ELIXIR Czech Republic and ELIXIR Netherlands came together in Maastricht for the first phase of a staff exchange designed to tackle a persistent challenge in the life sciences: how to better connect findings from toxicology and metabolomics. While both domains generate rich, complementary data, they often evolve in parallel and in a disconnected setting - using different tools, identifiers, and conceptual frameworks. During this exchange, researchers from RECETOX (Brno) and Translational Genomics (Maastricht) set out to change that.
Why this exchange matters to life science resources from across Europe
The initiative was built around three core goals:
1. strengthening a shared portfolio of interoperable tools and services,
2. facilitating knowledge transfer across nodes, and
3. improving integration between the metabolomics and toxicology communities.
At its heart lies the Adverse Outcome Pathway (AOP) framework - a structured way to represent biological mechanisms linking (molecular) events and stressors to adverse outcomes. By aligning AOP-based approaches with metabolomics workflows, the teams aim to enable more holistic analyses that connect chemical exposure, molecular changes, and biological effects.
From alignment to interoperability
Rather than starting from scratch, the exchange focused on deepening connections between existing tools. Technologies such as BridgeDb, IDSM, MSMetaEnhancer, WikiPathways, and FixID were central to discussions, with an emphasis on moving beyond basic compatibility toward full interoperability.
One particularly promising direction involves federated queries that bridge datasets and domains - for example, querying AOP knowledge bases using mass spectrometry (MS) data through integrations between IDSM and AOP-Wiki-RDF. This kind of cross-domain querying could significantly streamline how researchers link experimental metabolomics data to mechanistic toxicology knowledge.
Alongside identifier mapping and ontology alignment, participants explored how AI-driven tools can enhance data integration. Applications ranged from text mining (e.g., aoptk) to image-based knowledge extraction (e.g. PFOCR), highlighting how automation can help scale the interpretation of complex biological data and establish FAIR-compliant best practices.
Hands-on collaboration and concrete progress
The exchange was not just conceptual - it was highly practical. Working sessions focused on improving and extending key tools:
These efforts reflect a shared priority: making tools not only interoperable, but also easier to use in real-world workflows and scalable to answer new research questions.
Toward measurable impact and a more connected ELIXIR ecosystem
The collaboration is already shaping new research directions. Planned benchmarking studies will evaluate how well different tools perform in named entity recognition (NER) for small molecules, identifier resolution, and structural similarity analysis. These efforts will provide much-needed insight into how data interpretation varies depending on tools and identifiers - a key issue for reproducibility.
What makes this exchange particularly valuable is its broader impact. By reducing fragmentation and aligning tools and standards, we help both nodes operate more efficiently and demonstrate how shared infrastructure, open collaboration, and a focus on FAIR principles can close gaps and bring communities together. The second phase of the exchange, scheduled for later this year in Brno, will build on this momentum. If the first visit is any indication, the collaboration is well on its way to turning alignment into true integration - laying the groundwork for more powerful, cross-domain life science research.
Resources
The Stockholm Convention Regional Centre at RECETOX, with the support of the Ministry of Environment and Physical Planning of the North Macedonia and Ekomozaik, convened the Updated Stockholm Convention National Implementation Plan Endorsement Meeting.
On 25 February 2026, the Stockholm Convention Regional Centre (SCRC) at RECETOX convened the Updated Stockholm Convention (SC) National Implementation Plan (NIP) Endorsement Meeting in Sarajevo.
