[3dem] Distribution of Electron Microscopy metadata in PDBx/mmCIF file format
Justin Flatt
justin at rcsb.rutgers.edu
Fri Oct 6 07:23:37 PDT 2023
At the beginning of October 2023, the Electron Microscopy Data Bank
(EMDB) will start distributing electron microscopy (EM) metadata for its
entries in PDBx/mmCIF file format alongside the already available XML
formatted files. The addition of PDBx/mmCIF files in the archive will
bring parity between EMDB and PDB (EM experimental data vs 3D
structures) in the way metadata is served while improving the
consistency and interoperability between the two archives. EMDB entries
released before October 2023 will have PDBx/mmCIF files added at a later
date. The description of PDBx/mmCIF categories and items featured in EM
metadata files can be found in the PDBx/mmCIF dictionary
(https://urldefense.com/v3/__https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/em_group.html__;!!Mih3wA!H0K0mbiWqxoJ8iY7opuGwbv4ShCzUGt-hQaaPensMr9KYz8GN8ql5YeErIS-R7BKbXMK4oSJpESufg-vl2QsvUBa$ ).
For an EMDB entry EMD-xxxxx, PDBx/mmCIF file name will be
emd-xxxxx.cif.gz and it will be located in the entry's subfolder called
metadata (EMD-xxxxx/metadata) in the wwPDB archive repositories:
* EMDB: https://urldefense.com/v3/__https://ftp.ebi.ac.uk/pub/databases/emdb/structures/__;!!Mih3wA!H0K0mbiWqxoJ8iY7opuGwbv4ShCzUGt-hQaaPensMr9KYz8GN8ql5YeErIS-R7BKbXMK4oSJpESufg-vl2MZpXLK$
* wwPDB: https://urldefense.com/v3/__https://files.wwpdb.org/pub/emdb/structures/__;!!Mih3wA!H0K0mbiWqxoJ8iY7opuGwbv4ShCzUGt-hQaaPensMr9KYz8GN8ql5YeErIS-R7BKbXMK4oSJpESufg-vlxGtwnjO$
* RCSB PDB (US): https://urldefense.com/v3/__https://files.rcsb.org/pub/emdb/structures/__;!!Mih3wA!H0K0mbiWqxoJ8iY7opuGwbv4ShCzUGt-hQaaPensMr9KYz8GN8ql5YeErIS-R7BKbXMK4oSJpESufg-vlzOCzSnJ$
* PDBe (UK): https://urldefense.com/v3/__https://ftp.ebi.ac.uk/pub/databases/emdb/structures/__;!!Mih3wA!H0K0mbiWqxoJ8iY7opuGwbv4ShCzUGt-hQaaPensMr9KYz8GN8ql5YeErIS-R7BKbXMK4oSJpESufg-vl2MZpXLK$
* PDBj (Japan): https://urldefense.com/v3/__https://files.pdbj.org/pub/emdb/structures/__;!!Mih3wA!H0K0mbiWqxoJ8iY7opuGwbv4ShCzUGt-hQaaPensMr9KYz8GN8ql5YeErIS-R7BKbXMK4oSJpESufg-vl1lvb4mi$
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