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Using the Chemotion repository to deposit and access FAIR research data for chemistry experiments

Nature Protocols volume 20, pages 1097–1098 (2025)Cite this article

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Research data repositories can be used to securely archive and share results from scientific research. They are a crucial foundation for enabling transparent and reproducible science. For this reason, many funding organizations1 and journals require or recommend the use of repositories for depositing research data2. Depending on the discipline, repositories stipulate specific requirements for the deposited data, such as adhering to the FAIR (findable, accessible, interoperable, reusable) principles. Special challenges arise in the field of chemistry where reanalyzing data often requires machine-readable representation of chemical structures and digitally readable procedures.

The Chemotion repository3,4 was developed in 2014 to allow chemists and other scientists to share data from chemistry experiments in a reusable and traceable manner, incorporating ___domain-specific standards. While generic repositories can also be utilized by chemists, they may not fully support the typical structuring and visualization of chemistry data, and achieving machine readability of the data in these repositories can be challenging or only partly feasible5,6,7. With Zenodo, for example, molecular information is buried and cannot be synchronized with other databases.

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Fig. 1: Chemotion repository.

Data availability

Data published within the Chemotion repository can be accessed via the repository’s website: https://chemotion-repository.net/home/welcome.

Code availability

The source code for the Chemotion repository and Chemotion ELN is managed on two GitHub repositories (https://github.com/ComPlat/chemotion_REPO (repository) and https://github.com/ComPlat/chemotion_ELN (ELN)) and is available under open-source licenses. The latest Zenodo references for the Chemotion repository12 and Chemotion ELN13 link to the current status of both systems.

References

  1. Deutsche Forschungsgemeinschaft. Guidelines for safeguarding good research practice. Code of conduct. Zenodo https://doi.org/10.5281/zenodo.6472827 (2022).

  2. Publisher data availability policies index. CHORUS https://go.nature.com/4eXiICk (2024).

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Acknowledgements

We are thankful for the support of the Ministry of Science, Research and the Arts of Baden-Württemberg (MWK Baden-Württemberg, project MoMaF), which supported the development of Chemotion as part of the developments within the Science Data Center of the MWK. We further acknowledge the support of the Helmholtz research field information and the Karlsruhe Nano Micro Facility (KNMFi), which support the maintenance of the software Chemotion ELN. The results of this project could be achieved due to the support of the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) for the project NFDI4Chem (project number 441958208).

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Authors and Affiliations

  1. Institute of Biological and Chemical Systems, Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology, Karlsruhe, Germany

    Pei-Chi Huang, Chia-Lin Lin, Pierre Tremouilhac, Nicole Jung & Stefan Bräse

  2. Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany

    Nicole Jung & Stefan Bräse

Authors
  1. Pei-Chi Huang
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  2. Chia-Lin Lin
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  3. Pierre Tremouilhac
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  4. Nicole Jung
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  5. Stefan Bräse
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Contributions

C.-L.L., P.-C.H. and P.T. designed and implemented the technical processes of the Chemotion repository. All authors contributed to the conceptual work of this project and wrote the paper.

Corresponding authors

Correspondence to Pei-Chi Huang, Chia-Lin Lin, Nicole Jung or Stefan Bräse.

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The authors declare no competing interests.

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Huang, PC., Lin, CL., Tremouilhac, P. et al. Using the Chemotion repository to deposit and access FAIR research data for chemistry experiments. Nat Protoc 20, 1097–1098 (2025). https://doi.org/10.1038/s41596-024-01074-z

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