The EM Glossary: a community effort towards harmonized terminology in electron microscopy

Follow us on social media Brendike-Mannix, O.1; Schröder, R.R.2; Kühbach, M.3; Pauly, C.4; Aversa, R.5; Brockhauser, S.3; Azócar Guzmán, A.6; Özkan, Ö.1; Konijnenberg, P.J.6; Sandfeld, S.6 ; Sedeqi, M.1; Hebert, C.7; Hofmann, V.6 The EM Glossary: a community effort towards harmonized terminology in electron microscopy Our goal is to harmonize terminology in electron and ion microscopy so humans, devices and algorithms can collaborate more efficiently and effectively. We achieve this through four measures. Adoption support We offer extensive support for EM Glossary adoption. The NFDI FAIRmat consortium has adopted EM Glossary terminology via their NXem application definition for NeXus. These definitions have been implemented in the research data management platform NOMAD (Novel Materials Discovery). In this way the EM Glossary is being actively used by thousands of materials scientists. The Helmholtz Joint Lab Model and Data Driven Materials Characterization (JL-MDMC) and the Nanoscience Foundries and Fine Analysis Europe Pilot (NEP) have developed application-level metadata schema for transmission and scanning electron microscopy which reference EM Glossary terminology. These schemas have been registered in the NEP metadata repository ensuring the EM Glossary is integrated in European research infrastructure. NFDI-MatWerk has aligned with EM Glossary terminology in schemas registered in their metadata repository. 1Helmholtz Zentrum Berlin für Materialien und Energie, 14109 Berlin, Germany; 2Universitätsklinikum, Universität Heidelberg, BioQuant, 69120 Heidelberg, Germany; 3Humboldt Universität zu Berlin; Physics Department and CSMB, Zum Großen Windkanal 2, D12489 Berlin, Germany; 4Universität des Saarlandes, Funktionswerkstoffe, 66123 Saarbrücken, Germany; 5Karlsruhe Institute of Technology, Scientific Computing Center (SCC), Data Exploitation Methods, 76131 Karlsruhe; ⁶Forschungszentrum Jülich GmbH, Institute for Advanced Simulation – Materials Data Science and Informatics (IAS-9), 52068 Aachen, Germany; 7LSME, IPHYS, Ecole Polytechnique Féderalé de Lausanne, Switzerland Get involved Harmonized definitions for over 65 terms are provided as a machine-readable resource in the web ontology language (OWL1). Content developed with the community is mapped into class hierarchy and annotation properties. “emg.owl” base URI: purls.helmholtz-metadaten.de/emg. The artifact offers stable domain-level semantics and is regularly updated based on progress in our community group. The EM glossary is a collaboration between electron microscopists and metadata experts from over 23 institutions across Switzerland, the Netherlands, Austria, and Germany, as well as representatives of FAIRmat and NFDI-Matwerk. Development is an open and inclusive process with provenance captured in our GitLab repository. Easy browsing of the EM Glossary is provided by a web app. This provides additional context for the glossary and facilitates the use of the resource for technical writing or teaching purposes. Community Terminology Harmonisation Machine-readable OWL artifact EM Glossary Web Explorer This work was supported by the Helmholtz Metadata Collaboration (HMC), an incubator-platform of the Helmholtz Association within the framework of the Information and Data Science strategic initiative; and the NFDI consortia “MatWerk” and “FAIRmat”, funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 38/1 – project number 460247524 (MatWerk) & 460197019 (FAIRmat). Mission Sign up to our mailing list 1 https://www.w3.org/OWL/