OpenEM: Open research data infrastructure for electron microscopy in Switzerland

Abstract

The Open Electron Microscopy Data Network (OpenEM) is a Swiss-wide collaboration to improve data management at electron microscopy (EM) facilities and make the dissemination of EM data open and FAIR (findable, accessible, interoperable, and reusable). The collaboration is based around a central SciCat instance hosted at the Paul Scherrer Institute (discovery.psi.ch), which stores metadata from all facilities and provides data access and management to microscope users, facility managers, and the public. 

Electron microscopy has become an essential tool in structural biology and other fields, with modern microscopes producing above 10 TB per day. Managing these datasets is challenging for researchers and facilities producing the data. Making the data publicly accessible is also difficult due to limited integration of existing databases with the EM infrastructure, as well as a lack of repositories for all use cases.

The OpenEM project aims to improve this by providing a central repository for all EM data and metadata from EM facilities in Switzerland. Metadata schemas are under development as part of the Open Science Community for EM, in cooperation with other community-driven ontologies such as PDBx/mmCIF, the EM Glossary, NXem, and the cryoEM ontology. Data is stored on tape at the Swiss National Supercomputing Centre (CSCS) or the ETHZ Long-Term Storage, from which it can be retrieved by collaborators and the public. 

Interoperability with other data repositories is a priority, particularly the EMDB and EMPIAR databases for macromolecular data. The OpenEM infrastructure aims to streamline the full data lifecycle for EM data, from data collection through publication and reuse.