EMDB and EMPIAR have moved

What has changed?

On 21 July 2021, EMDB and EMPIAR moved “home”. EMDB has moved to www.ebi.ac.uk/emdb and EMPIAR to www.ebi.ac.uk/empiar. In the case of EMDB, the change was accompanied by the release of a completely redesigned website that constitutes a major improvement over the old one. The changes mean that you may need to change some of your bookmarks in your browser(s), or links to EMDB and EMPIAR pages that you may have on webpages that you maintain.

What will happen next?

We will maintain the old websites until early August 2021. Once we are confident that there are no major issues with the new websites, the old ones will be switched off. We will then put redirects in place for old pages to their equivalent new location. (Due to the new functionality and organisation of the EMDB website, this may not always be possible, but will happen on a best-effort basis.) These redirects may at a later stage be deprecated; this will be communicated at that time.

What do I need to do?

We strongly recommend changing any and all links and bookmarks from the old to the new locations as soon as possible.

There has been an EMDB API for several years. This has been maintained by the PDBe team and will continue to be maintained for the foreseeable future. However, with the advent of its new website, EMDB itself now also provides an API which gives access to a superset of the information available from the older API as well as access to searches of EMDB and EMPIAR. We therefore recommend all API users to migrate to the new EMDB-provided API. For any queries about the API please contact the EMDB helpdesk.

The table below shows examples of old URLs and corresponding new URLs:

Description Old URL New URL Shortcut
EMDB main page www.ebi.ac.uk/pdbe/emdb www.ebi.ac.uk/emdb emdb-empiar.org
EMDB entry page (example) www.ebi.ac.uk/pdbe/entry/emdb/EMD-1001 www.ebi.ac.uk/emdb/entry/EMD-1001 emdb-empiar.org/EMD-1001
EMDB API documentation www.ebi.ac.uk/pdbe/api/doc/emdb.html www.ebi.ac.uk/emdb/api/ emdb-empiar.org/api/
EMDB API entry (example) www.ebi.ac.uk/pdbe/api/emdb/entry/all/EMD-1001 www.ebi.ac.uk/emdb/api/entry/EMD-1001 emdb-empiar.org/api/entry/EMD-1001
EMstats www.ebi.ac.uk/pdbe/emdb/statistics_main.html/ www.ebi.ac.uk/emdb/statistics emdb-empiar.org/statistics
EMPIAR main page www.ebi.ac.uk/pdbe/emdb/empiar www.ebi.ac.uk/empiar empiar.org
EMPIAR entry page (example) www.ebi.ac.uk/pdbe/emdb/empiar/entry/10002 www.ebi.ac.uk/empiar/entry/10002 empiar.org/EMPIAR-10002
EMPIAR API documentation www.ebi.ac.uk/pdbe/emdb/empiar/api/documentation/ www.ebi.ac.uk/empiar/api/documentation/ empiar.org/api/documentation/
EMPIAR API (entry) www.ebi.ac.uk/pdbe/emdb/empiar/api/entry/EMPIAR-10050 www.ebi.ac.uk/empiar/api/entry/EMPIAR-10050 empiar.org/api/entry/EMPIAR-10050
EMPIAR deposition system www.ebi.ac.uk/pdbe/emdb/empiar/deposition/ www.ebi.ac.uk/empiar/deposition/ empiar.org/deposition

What else has changed for EMDB?

The EMDB website was redesigned from scratch, based on the outcomes of a user survey with over 100 participants who provided useful input about what they liked about the old website, what they didn’t like, and what new features they would like to see. The new website has a modern look and feel, improved usability and introduces many new features that have been requested by users. The EMDB databases use the latest EMDB data model, which means a lot more information about the structures can now be shown on the entry pages. This data model was also used to design a completely new search engine which allows users to create precise queries and to generate customised graphs about their search results, using integrated data from EMDB and EMPIAR. EMstats now include 75 predefined charts (up from 30 graphs previously). For power users, the REST API includes the same endpoints as the old version but returns a lot more information thanks to the latest data model. There are also new endpoints, e.g. to allow fetching complete EMDB entry metadata or to perform advanced searches on EMDB and EMPIAR.

Questions and feedback

If you have any questions (or want to report any issues, or have any other feedback) regarding these changes, please contact the EMDB helpdesk or the EMPIAR helpdesk.