Distribution of Electron Microscopy metadata in PDBx/mmCIF file format

JY
Jasmine Young
Fri, Oct 6, 2023 2:21 PM

Dear PDB-l,

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://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/em_group.html).
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:

http://www.wwpdb.org/news/news?year=2023#top

--
Regards,

Jasmine

---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320

---==========================

Dear PDB-l, 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://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Groups/em_group.html). 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://ftp.ebi.ac.uk/pub/databases/emdb/structures/ * wwPDB: https://files.wwpdb.org/pub/emdb/structures/ * RCSB PDB (US): https://files.rcsb.org/pub/emdb/structures/ * PDBe (UK): https://ftp.ebi.ac.uk/pub/databases/emdb/structures/ * PDBj (Japan): https://files.pdbj.org/pub/emdb/structures/ <http://www.wwpdb.org/news/news?year=2023#top> -- Regards, Jasmine =========================================================== Jasmine Young, Ph.D. Biocuration Team Lead RCSB Protein Data Bank Research Professor Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8087 Email:jasmine@rcsb.rutgers.edu Phone: (848)445-0103 ext 4920 Fax: (732)445-4320 ===========================================================