wwPDB to switch to v3 EMDB data model

From February 9, 2022, the wwPDB EMDB Core Archive will exclusively support version 3 of its data model and retire version 1.9.6 header files from the archive. The switch will involve several changes regarding file provision by the archive and this article outlines these changes.

Since the inception of OneDep in 2015, the EMDB Core Archive (EMBL-EBI: https://ftp.ebi.ac.uk/pub/databases/emdb/, PDBj: https://ftp.pdbj.org/pub/emdb/, wwPDB mirror site: https://ftp.wwpdb.org/pub/emdb/) has maintained two versions of its data model in parallel and also two versions of the header file for each entry. Currently, the official EMDB data model is version 1.9.6, while version 3, which facilitates a richer representation of the metadata about EMDB entries, was introduced in 2015.

Version 3 has now been finalized, and EMDB will therefore change its official data model version from v1.9.6 to v3. This will involve three changes to the EMDB Core Archive as of February 9, 2022:

1. The current EMDB data model, defined in an XSD schema in a file named emdb.xsd and located in /doc/XML-schemas/emdb-schemas/current/, will change to the latest version of the v3 data model (at present v3.0.2.6).
2. The official header file for each entry in the EMDB Core Archive, an XML file named emd-xxxxx.xml, will become a v3 XML file that follows the structure of the latest version of the v3 data model.
3. The EMDB Core Archive will cease provision of v1.9.6 header files for all entries.

Currently, for an entry EMD-xxxxx in the EMDB core archive located at /structures/EMD-xxxxx/header/, the following header files are provided:

1. Official header file: emd-xxxxx.xml
2. Header file for data model v3: emd-xxxxx-v30.xml
3. Header file for data model v1.9.6: emd-xxxxx-v19.xml

where emd-xxxxx.xml at present is a copy of the file emd-xxxxx-v19.xml, adhering to v1.9.6 of the EMDB data model.

From 9th February 2022 onward, for any entry, the following header files will be provided:

1. Official header file: emd-xxxxx.xml
2. Header file for data model v3: emd-xxxxx-v30.xml

where emd-xxxxx.xml will be a copy of emd-xxxxx-v30.xml, supported by v3 of the EMDB data model.

For any further information please email info@wwpdb.org.

Source: wwPDB News 6 August 2021

Note: EMDB is now an official partner in the Worldwide PDB. See wwPDB News 24 June 2021