A community-driven glossary for data interoperability in the electron microscopies

Abstract text (incl. figure legends and references)

Research data has to fulfil a number of requirements for it to be fully exploitable - today and in the future. The FAIR principles [1] – findable, accessible, interoperable, and reusable – provide a conceptual framework to achieve this, but the pathway to implementation is often unclear.

Here we focus on the challenge of implementing the "I" in FAIR. Interoperability is the potential for two independent agents to work on the same data in a coordinated fashion. It is especially relevant for researchers working in interdisciplinary fields, such as electron microscopy, where terminology in adjacent scientific disciplines is unknown, or where identical terms are used with differing meaning, for example, consider a mathematical or biological cell.

The use and adoption of established vocabularies and semantic standards can provide solutions – however these may be infeasible to implement, non-existent, or scientifically unsuitable. This is why a number of initiatives are developing semantic artefacts that aim to describe experimental equipment, workflows, and analysis procedures in electron and ion microscopies. Harmonisation of these efforts to ensure interoperability across the community is required.

To support the long-term semantic interoperability the Helmholtz Metadata Collaboration (HMC) is coordinating a community-wide effort, including over 45 scientists from more than 22 institutions across Switzerland, Austria, and Germany, and including representatives of several NFDI consortia [2], to create a joint resource to harmonize semantics in the field of electron and ion microscopies. In our presentation we will report on this community effort - the EM glossary group [3]. We will describe how we achieve consensus on terms commonly used in electron and ion microscopies via a remote, collaborative workflow based on the platform GitLab. A text-mining approach has been used to evaluate EM image metadata and prioritise terms which are widely used in the community. We will show results, including some of our harmonized definitions, and provide details of our implementation strategy.

The developed resource will provide harmonized and machine actionable semantics to support specific development efforts such as metadata schemas or ontologies in their respective fields. This will benefit experimental scientists by providing clarity when annotating and re-using research data; and by facilitating communication when conducting interdisciplinary studies.

Do you work in electron and/or ion microscopy or related data analysis? Follow us on twitter @helmholtz_hmc or tweet #EMGlossary. You want to get involved in the development and/or join our meetings? Send an email to hmc@fz-juelich.de or hmc-matter@helmholtz-berlin.de

1. Wilkinson, M.D. et al. Scientific Data. http://dx.doi.org/10.1038/sdata.2016.18 (2016)

2. NFDI: Nationale Forschungsdateninfrastruktur. https://www.nfdi.de/

3. EM Glossary GitLab repository: https://codebase.helmholtz.cloud/em_glossary/