Completed Cells, Biochemistry & Physiology Genetics & Molecular Biology

EMDB: dealing with the cryo-EM data deluge

In plain English

AI plain-English summary

Cryo-electron microscopes are generating data faster than the world’s sole archive for their 3D reconstructions can handle. The Electron Microscopy Data Bank (EMDB), run by EMBL-EBI and international partners, stores the 3D structures of molecules and cells captured by cryo-EM—a technique that won the 2017 Nobel Prize in Chemistry. As new improvements like phase plates and robotics accelerate data production, the archive faces a deluge of larger, more complex files. Without upgrades, researchers could lose access to validated, searchable data that underpins discoveries in structural biology. This project will expand EMDB’s capacity to handle growing volume and diversity. It will enrich entries with biological annotations using crowd-sourcing and machine learning, develop validation tools to ensure data quality, and build better web resources for searching and visualising structures. These improvements will also help other bioinformatics databases integrate EMDB data. If successful, the work will keep a critical piece of scientific infrastructure running smoothly. It will not change daily life directly, but it will ensure that the fundamental science of molecular structure—which has already enabled drug design and vaccine development—continues to rely on a robust, accessible archive.

View original technical description
Decades of research (rewarded with the 2017 Nobel Prize in Chemistry) have led to revolutionary developments in the field of cryo-electron microscopy (cryo-EM), with further improvements underway (phase plates, robotics). The Wellcome Trust and other funders have recognised the importance of cryo-EM and made substantial investments in infrastructure. These developments together cause a vast increase in the amount and diversity of experimental data emanating from molecular and cellular structural studies. EMDB (Electron Microscopy Data Bank), maintained by EMBL-EBI with international partners, is the single global archive of 3D cryo-EM reconstructions. This project will address major archiving challenges caused by the rapid growth of the cryo-EM field. Its aims are: 1. Handling the increasing volume, complexity and diversity of EM data depositions. 2. Data enrichment and validation - by enriching EMDB entries with biological annotations, expanding the volume of biologically-annotated segmentations in EMDB by exploiting crowd-sourcing initiatives and machine-learning techniques and developing and maintaining validation tools and resources for EMDB. 3. Enabling effective use of EMDB data - by developing new and improved web-based resources for searching, analysing and visualising EMDB data and developing tools and resources that facilitate the use of EMDB data by other bioinformatics resources.

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Researchers

Ardan Patwardhan (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

The Electron Microscopy Data Bank
A2O - Transforming EMPIAR into an Essential Resource for EM Data Spanning Scales from Atoms to Organisms
Integrating 3D biological data on scales from molecules to cells
Handling complexity in huge heterogeneous cryo electron microscopy datasets: visualising biological processes at quasi-atomic resolution
Collaborative Computational Project for cryo electron microscopy (CCP-EM): expanding the reach of cryoEM

Original classification

Biomedical Resources Grant

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