Documentation

Summary

EMDB documentation pages are indexed below. These documents are intended to provide user focused guidance on systems and services that are provided by the EMDB or by our partners through our services, in particular our partners of the wwPDB.

Table of contents

  1. General
    1. EMDB data model
    2. Policies
  2. Deposition (OneDep)
    1. General deposition
    2. Composite map deposition
  3. EMDB Services
    1. Search engine
    2. Chart builder
    3. EMICSS
    4. Validation Analysis
    5. API
  4. Miscellaneous
    1. FAQ
    2. Selected Publications

Contact us

Getting in touch: if anything he needs clarification, please reach out to us at the EMDB helpdesk. Important: for any matters related to an active deposition, please only reach out to us through the OneDep deposition system in the communication module of your active deposition.

General

EMDB data model

Data models which describe entries in the database are maintained by the EMDB and the wwPDB. Users will find two data models in which metadata information on database entries can be found, XML and CIF. In practise, for supplying metadata directly to a deposition, users and software developers should use CIF.

→ View data model documentation

Policies

EMDB policies are developed to convey policies specific to our systems and services. Where the EMDB is a core member of the wwPDB consortium, our EMDB policies were developed to complement wwPDB policies. Our processes are governed by both policy documents and are under continuous review to harmonise them.

→ Read EMDB policies

→ View wwPDB policies

Deposition (OneDep)

General deposition

The EMDB maintains a general deposition guide. This document is complimentary to basic OneDep deposition information here. In cases of uncertainty please contact us.

→ Read general deposition guide

→ Open OneDep general deposition guide

Composite map deposition

Depositors can find a guide with specific guidance on how to approach the submission of composite maps and their constituent consensus and focus refinements. This guide aims to provide a strategy for completing this kind of deposition efficiently whilst aligning the entries with community derived policy on composite maps.

→ Read composite map deposition guide

EMDB Services

Search engine

Search of the EMDB is powered by Solr provided by EBI. This drives the search functionality of the website but also up-to-date entry page cross referencing. The system can be utilized to create queries that return archive wide metadata.

→ Explore search engine documentation

→ Check the list of available search fields

Chart builder

Built on top of EMDB search, specialized queries are made by the EMDB Chart Builder to plot archive wide metadata and derivative analyses in live interactive charts.

→ Learn how to use the Chart Builder

EMICSS

This system uses data provided at the point of deposition to systematically search associated databases for information which may be used to enrich the annotations of entries.

→ Learn how EMICSS works

Validation Analysis

The validation pipeline developed by the EMDB for 3DEM data and associated model coordinates generates validation data for entries when they are deposited to the wwPDB via OneDep. These are the validation data that are communicated to manuscript peer reviewers via the wwPDB PDF validation report. Additional validation data are generated upon data release (normally upon manuscript publication) and communicated to the public via EMDB entry pages on the validation tab.

→ View validation analysis documentation

API

The EMDB Application Programming Interfaces (APIs) provide rapid, scalable and automatable access to 3DEM reconstruction metadata and data. The APIs currently are dedicated to serve (1) main archive, added-value (2) quality validation and (3) semantic annotation metadata and data. A python wrapper provides unified access to selected endpoints across all of the APIs. 

→ View API documentation

Miscellaneous

Frequently Asked Questions (FAQ)

Answers to common questions about EMDB data, deposition, services, and policies.

→ Browse frequently asked questions

Selected Publications

  • Fonseca, N., et al. (in press). Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank. Frontiers
  • Pintilie, G., et al. (2025). Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps. Acta Cryst. D. doi.org/10.1107/S2059798325005923
  • Duraisamy, A. K., et al. (2025). EMICSS: Added-value annotations for EMDB entries. Bioinformatics Advances. doi.org/10.1093/bioadv/vbaf203
  • Kleywegt, G. J., et al. (2024). Community recommendations on cryoEM data archiving and validation. IUCrJ. doi.org/10.1107/S2052252524001246
  • The wwPDB consortium., (2024). EMDB - the Electron Microscopy Data Bank. Nucleic Acids Research. doi.org/10.1093/nar/gkad1019
  • Patwardhan, A., et al. (2017). Building bridges between cellular and molecular structural biology. eLife. doi.org/10.7554/eLife.25835
  • Patwardhan, A., et al. (2014). A 3D cellular context for the macromolecular world. Nature Structural & Molecular biology. doi.org/10.1038/nsmb.2897
  • Patwardhan, A., et al. (2012). Data management challenges in three-dimensional EM. Nature Structural & Molecular Biology. doi.org/10.1038/nsmb.2426

Under development

Segmentation data model prototype.

→ Find out more about this project