An ontology-based description of nano computed tomography measurements in electronic laboratory notebooks

F. Kirchner, D.C.F. Wieland, S. Irvine, S. Schimek, J. Reimers, R. Aversa, A. Boubnov, C. Lucas, S. Flenner, I. Greving, A. Lopes Marinho, T. M. Wong, R. Willumeit-Römer, C. Eschke, B. Zeller-Plumhoff

Abstract

Scientific communities have recognized the importance of well-documented metadata generated during research. However, ensuring that metadata is findable, accessible, interoperable, and reusable (FAIR) remains a significant challenge. To address this, scientific communities are working towards making metadata available in semantically annotated knowledge graphs using semantic web technologies. In our proposed solution, the creation of a schema is initiated at the very beginning of the scientific process. This is transformed into a data collection platform using the electronic laboratory notebook framework, Herbie, which facilitates the automatic validation and semantic annotation of metadata. Using the example of synchrotron-radiation-based nano-computed-tomography measurements at a beamline, we demonstrate this approach. It effectively captures the complex metadata of such research instruments along with their various configurations, providing a user-friendly experience. We illustrate how Herbie converts all semantic documents into a user interface, ensuring that the entered data automatically meets all FAIR requirements. Additionally, we show how data can be extracted from the knowledge graph using SPARQL queries.

Resources

[pdf] [arxiv]

Bibtex

@article{kirchner2026ontology,
    title={An ontology-based description of nano computed tomography measurements in electronic laboratory notebooks},
    author={Kirchner, F and Wieland, DCF and Irvine, S and Schimek, S and Reimers, J and Aversa, R and Boubnov, A and Lucas, C and Flenner, S and Greving, I and others},
    journal={Scientific Data},
    year={2026},
    publisher={Nature Publishing Group UK London}
}