How the MetaboLights repository can help you to put Open Science into practice in metabolomics research

<h2>Introduction</h2><p dir="ltr">This repository item contains the teaching design and the teaching materials for a workshop on Open Science and the MetaboLights repository that was given at the Chemical Biological Centre (KBC) at Umeå University and the Swedish University of Agricultural Sciences (SLU) on 19 March 2025 (Kieselbach, 2025).</p><p dir="ltr">The goal of this workshop was to give researchers and PhD students who use metabolomics in their research an opportunity to learn about the importance of Open Science policies for the preparation of their scholarly publications. In addition, this workshop offered them an opportunity to learn how they can use the MetaboLights repository at EMBL-EBI (Yurekten et al., 2024) to turn their research data from metabolomics studies into citable research outputs that comply with the FAIR-data guiding principles (Wilkinson et al., 2016).</p><p dir="ltr">For the documentation of the teaching design and the teaching materials, we used the templates by Clare et al. (2022).</p><h3>Desired learning outcomes</h3><p dir="ltr">1. Participants understand that publishing manuscripts with an Open Access license is not sufficient to fully comply with policies for Open Science.</p><p dir="ltr">2. Participants understand that the preparation of scholarly manuscripts needs to be aligned with the preparation of catalog posts about the research data that are the basis for them.</p><p dir="ltr">3. Participants know the purpose of the FAIR-data principles and how they can use a trusted repository to create FAIR-data.</p><p dir="ltr">4. Participants know the principal structure of the MetaboLights database and what kind of data it contains.</p><p dir="ltr">5. Participants know which sections the description of a study in MetaboLights contains. For example, general information, protocols, samples, assays, metabolites and data files.</p><p dir="ltr">6. Participants know the search tools of the MetaboLights database and how one can use them to search for studies, species and compounds.</p><p dir="ltr">7. Participants know how to search in the database of Chemical Entities of Biological Interest (ChEBI).</p><p dir="ltr">8. Participants know how to create an account and a submission at MetaboLights.</p><p dir="ltr">9. Participants understand the principal parts of a submission to MetaboLights that includes the description of an assay, the samples, the metabolites and uploading the raw data files.</p><p dir="ltr">10. Participants know how to contact the MetaboLights Support Team to get help.</p><h3>Further information</h3><p dir="ltr">As for further details of the teaching design and the teaching material, please read the Readme-document of this entry.</p><h3>References</h3><p dir="ltr">1. Clare, H., Cepinskas, L. and Yates, K. (2022). Module 2. Design training in easy steps. Zenodo. https://doi.org/10.5281/zenodo.5840165</p><p dir="ltr">2. Kieselbach, T. (2025). Program and abstracts of the conference Current Trends in Applied Mass Spectrometry at the KBC Umeå on March 19th and 20th, 2025. Umeå University. Online resource. https://doi.org/10.17044/scilifelab.24230197.v1</p><p dir="ltr">3. Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. <i>Scientific data</i>, <i>3</i>, 160018. https://doi.org/10.1038/sdata.2016.18</p><p dir="ltr">4. Yurekten, O., Payne, T., Tejera, N., Amaladoss, F. X., Martin, C., Williams, M., O’Donovan, C. (2024). 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