The EM Glossary: a community effort towards a harmonized terminology in electron microscopy
Creators: name: Brendike-Mannix, Oonagh
name: Hofmann, Volker
name: Pauly, Christoph
name: Kühbach, Markus
name: Wollgarten, Markus
name: Konijnenberg, Peter
name: Schröder, Rasmus R.
name: Aversa, Rossella
name: Brockhauser, Sandor
name: Özkan, Özlem
name: Azócar Guzmán, Abril
name: Sedeqi, Mojeeb Rahman
name: Sandfeld, Stefan
Publisher: name: Karlsruher Institut für Technologie (KIT)
Year: 2024
Subjects: Electron microscopy
Glossary
Ontology
FAIR data
Metadata Harmonization

description: To be fully exploitable and ‘future proof’, research data needs to meet various requirements. For this, the FAIR principles [1] – Findable, Accessible, Interoperable, and Reusable - provide a widely accepted framework.

Here, we want to focus on ‘interoperability’, which requires a common language for knowledge representation within interdisciplinary fields, such as electron microscopy (EM). Such semantic standards are often lacking or even controversial. In the field of EM, a number of application-level initiatives independently started developing metadata schemas [e.g. 2,3], to describe experimental equipment, workflows, and analysis procedures. Semantic harmonisation of such efforts is required to ensure data interoperability in the future. As a first step, misalignment of terminology has to be addressed by mapping concepts of different scientific contexts, and user groups.

The Helmholtz Metadata Collaboration (HMC) [4] is currently coordinating a first effort, the EM glossary group [5], to establish a documented terminology for electron and ion microscopy (IM). This community involves scientists from more than 23 institutions across Switzerland, Austria, and Germany and representatives of the FAIRmat and the MatWerk NFDI consortia.

In a remote collaborative workflow and bi-weekly online meetings, we work towards formulating consensus on terms that are commonly used in the EM and IM communities. We aim to produce concise, unpacked definitions with rich annotations in accordance with semantic best practices.

By now, we provide harmonized definitions for more than 60 terms which can be explored via a web interface [6]. In a next step, the glossary will be implemented as a machine accessible resource in the web ontology language (OWL) [7]. Both these representations are intended as a central resource to map and align application-level semantics, thereby acting as semantic glue within the field.

Ar you interested to get involved? See [5] and send an email to hmc@fz-juelich.de to get in touch!

 

References:

[1] Wilkinson, M.D. et al. Scientific Data. https://dx.doi.org/10.1038/sdata.2016.18
[2] Könnecke, M, et al. Journal of applied crystallography https://doi.org/10.1107/S1600576714027575
[3] Joseph, R, et al. https://doi.org/10.5445/IR/1000141604
[4] Helmholtz Metadata Collaboration: https://helmholtz-metadaten.de/en
[5] EM Glossary Group https://go.fzj.de/EMG-repo (development repository)
[6] EM Glossary User Interface: https://emglossary.helmholtz-metadaten.de (frontend)
[7] EM Glossary OWL: https://owl.emglossary.helmholtz-metadaten.de (OWL artifact)