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A comprehensive policy and procedures document for the EMDB archive has been drawn up by the EMDB team in order to ensure consistent and coherent rules for its data. The document is now available to view on the EMDB website.

Since its foundation in 2002, the Electron Microscopy Data Bank (EMDB; https://emdb-empiar.org/) archives publicly available three-dimensional (3D) electron cryo-microscopy (cryo-EM) maps and tomograms of biomacromolecules, their complexes and cellular structures. Following the release of the first eight EMDB entries in 2002, the EMDB archive grew steadily and currently stands at almost 10000 released maps. From 2016, EMDB entries are deposited and processed through the wwPDB OneDep system while the biocuration workload is shared geographically by the EMDB, PDBe, RCSB PDB and PDBj teams.

The policy outlines the requirements for data deposition, accepted formats, entry modifications and release. For example, the policy recommends for single-particle depositions to include a primary map (as shown in the accompanying publication), a raw map (unmasked, unfiltered, unsharpened) and unmasked half-maps, as well as any auxiliary files such as Fourier Shell Correlation (FSC) data. In the document EMDB also advises that the official wwPDB validation report generated after biocuration, which now includes EM map/tomogram validation and, if applicable, map-model validation, is provided to journal editors and referees as part of the manuscript submission and review process.

In response to the cryo-EM community’s increasing demand to make all data publicly available, EMDB strongly encourages the deposition of all atomic models to the Protein Data Bank (PDB), all 3D EM reconstructions to EMDB and all raw data (including tilt series for tomograms) to the Electron Microscopy Public Image Archive (EMPIAR ). Related entries in these archives reference one another, making the deposited data easily discoverable and accessible to the community.

The EMDB team and its umbrella organisation wwPDB, welcome feedback from EMDB users and depositors on the policies and procedures through emdbhelp@ebi.ac.uk.

[ wwPDB News ]

Created: 2020-01-14 (last edited: 1 month ago)2020-01-14