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Metabolomics and Lipidomics research workflows span from quantifying and identifying small molecules in mass spectrometry data. The results can be statistically analysed, and their biochemistry needs to be contextualised within pathways and metabolic networks. The EDAM ontology is a central semantic backbone for the ELIXIR ecosystem, organised into four top-level branches that describe different aspects of bioinformatics resources: Operations (what tools do), Data (the information being processed), Formats (how data are represented), and Topics (the scientific domains and areas of interest). Together, these branches provide a semantic framework that enables consistent annotation, discovery, interoperability, and integration of bioinformatics tools, workflows, and datasets.
Recent domain-driven EDAM extensions have been developed by different communities and initiatives. The mzTab-M data format was overhauled towards mzTab-M 2.1, which is ready for real-world implementation now as part of the Biohackathon Europe 2025. While several reader and writer libraries now support mzTab-M, not all relevant tools make use of this updated data standard. On bio.tools, only one tool is annotated as supporting mzTab-M. Galaxy is one of the main engines for the user-friendly development of workflows in ELIXIR and beyond, with more than 4k tools on the de.NBI powered usegalaxy.eu. Currently, ~75 of these tools are annotated with the EDAM Laboratory technique “Metabolomics”. The development of Galaxy workflows for metabolomics and lipidomics applications has seen a recent revival, and several tools were updated, and new tools created.
This project aims to bring these activity streams together with the following core objectives: implementing mzTab-M across several Galaxy tools for metabolomics and lipidomics, improving the EDAM and bio.tools annotations for these tools, and enhancing the Galaxy user experience aiding tool selection. The project plan consists of work packages that are partially independent of each other and will depend on the final project participants and their expertise:
- EDAM Ontology Improvements: Goals include i) the identification of overlapping or missing terms and alignment of definitions and properties for lipidomics and metabolomics, and ii) harmonization regarding practical aspects of domain-specific package annotations (e.g. application - technology - methodology combinations divide).
- mzTab-M Integration & Curation: We will 1) create a ranked list of high-priority curation targets in bio.tools and Galaxy tools to improve the annotation and discoverability of tools with mzTab-M support, and 2) extend some of the tools to add mzTab-M support.
- Galaxy & EDAM Ecosystem Integration (Stretch Goal): Contribute to a two-way improvement regarding the integration of Galaxy and EDAM—by supporting improvements to the EDAM-based Galaxy Tool Panel view, including EDAM annotations in workflow metadata on WorkflowHub (ultimately tagging Galaxy workflows with EDAM topics), and updating the Community Usage section in the EDAM Browser with Galaxy tools leveraging EDAM annotations, enabling semantic Galaxy tool and workflow discoverability at multiple endpoints.
The above work packages should appeal to a broad range of biohackathon participants with different expertise, ranging from semantic aspects to implementing improved interoperability for metabolomics and lipidomics research.