The Open Data Network for Electron Microscopy (OpenEM): ETH-ORD Establish presentation 2024
Description
Update on the OpenEM project.
The OpenEM project aims to enhance open data management practices within the Swiss electron microscopy (EM) community. Electron microscopes generate vast amounts of image data that have wide-ranging applications in fields such as structural biology, cell biology, and material science. OpenEM seeks to provide access to this data through a standardized, open, and interoperable repository consistent with FAIR data principles (Findable, Accessible, Interoperable, Reusable). This approach benefits the scientific community by streamlining data collection and publication workflows, ensuring tighter integration with established repositories, and promoting the reproducibility, verifiability, and reuse of datasets for new scientific discoveries. Open data can be reused for purposes far beyond those envisioned by the original authors, such as training AI models, refining results using newly developed methodology, or aggregating information from multiple datasets.
Central to this initiative is the SciCat data catalog, operated by the Paul Scherrer Institute (PSI), which is being expanded to serve as the primary repository for all open EM datasets. This encompasses platforms within both the ETH domain (EPFL, PSI, ETH Zurich, Empa) and swissuniversities (UNIGE, UNIBA, UNIBE, and UNIL). EM data and metadata from all participating facilities are collected in a standardized and efficient manner and then deposited into SciCat according to standards developed jointly with the international EM community. This centralized repository makes the data accessible to collaborators and the public, facilitating broader scientific engagement and discovery. Additionally, life science data can be easily deposited into international repositories such as the Electron Microscopy Database (EMDB), the Electron Microscopy Public Image Archive (EMPIAR), and the Protein Databank (PDB), further enhancing data accessibility and reuse.
OpenEM will bring the estimated 6.4 petabytes of EM data generated each year by Swiss EM facilities into the central data catalog. From there researchers can publish their datasets and make them available to other researchers, search engines, and the public. The project's commitment to open data principles ensures that the wealth of EM data can be leveraged to drive innovation and accelerate discoveries across structural biology, cell biology, material science, and beyond.
OpenEM is supported by the Open Research Data Program of the ETH Board.
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Additional details
Dates
- Submitted
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2024-06-13