[3dem] New Syntax for PDB DOIs for Entries Released After July 21, 2027

[Justin Flatt]

On July 21, 2027, the wwPDB will fully transition to extended 
12-character PDB IDs, the PDBx/mmCIF format, and the re-organized PDB 
archive [1]. At this point, new 4-character IDs will no longer be 
issued.

PDB Digital Object Identifiers (DOI) can be used to link to the 
corresponding wwPDB DOI landing page. DOIs are unique, persistent 
alphanumeric string assigned to digital objects to provide a permanent, 
reliable link to their location online. DOIs will not change once 
assigned.

The DOI syntax for PDB entries after July 20, 2027 will reflect the 
extended PDB ID.

DOIS FOR PDB ENTRIES DEPOSITED AFTER JULY 20, 2027 (ONLY ASSIGNED 
12-CHARACTER PDB IDS)

PDB entries that will only be issued extended PDB IDs (e.g., 
pdb_1000axyz), will have the same PDB ID in both 
`_database_2.database_code` and `_database_2.pdbx_database_accession` 
data items.

These entries will have a new PDB DOI format based on the extended PDB 
ID, e.g., 10.2210/pdb_1000axyz/pdb.

All 12 characters, including the pdb_ prefix, are included.

loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB pdb_1000axyz pdb_1000axyz 10.2210/pdb_1000axyz/pdb

DOIS FOR PDB ENTRIES DEPOSITED BEFORE JULY 21, 2027 (ASSIGNED BOTH 4- 
AND 12-CHARACTER PDB IDS)

The PDB DOI, 4-character PDB ID, and extended 12-character PDB ID are 
stored in the `database_2` category of the PDBx/mmCIF model file:

loop_
_database_2.database_id
_database_2.database_code
_database_2.pdbx_database_accession
_database_2.pdbx_DOI
PDB 1ABC pdb_00001abc 10.2210/pdb1abc/pdb

For these entries, the PDB DOI format with "pdb" prefix remains 
unchanged, e.g., 10.2210/pdb1abc/pdb.

For example, the PDB entry with ID 8y9m (and extended PDB ID 
pdb_00008y9m) has the DOI https://urldefense.com/v3/__https://doi.org/10.2210/pdb8y9m/pdb__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIkEXEdbl$ .

CITING PDB DOIS

Many journals use PDB DOIs to link to PDB data from published articles.

PDB DOIs are also used as citations for entries that are not associated 
with a primary citation.

  	* PDB DOIs are also used as citations for entries that are not 
associated with a primary citation.
  	* Entries that have been issued a 4-character ID (meaning it has been 
deposited before July 21, 2027) should be cited using the ID and DOI 
syntax for 4-character IDs (e.g., 10.2210/pdb1abc/pdb). This includes 
structures with extended IDs created from 4-character IDs using the 
prefix "pdb_0000" (e.g., "2abc" for pdb_00002abc)
  	* Entries that have only been issued a 12-character ID (meaning it has 
been deposited after July 20, 2027) should be cited using the new ID and 
DOI syntax (e.g., 10.2210/pdb_1000axyz/pdb)

For any further information please contact us at info at wwpdb.org.

TRANSITION RESOURCES

  	* PDB ID Extension FAQ [2]
  	* PDB Beta Archive Overview [3]: includes scripts, shortlink URLs, and 
other resources
  	* Understanding PDBx/mmCIF format [4]
  	* PDBx/mmCIF User Guide [5]
  	* PDBx/mmCIF Dictionary [6]
  	* PDB -> PDBx/mmCIF correspondences [7]
  	* An online PDBx/mmCIF Editor [8]
  	* PDBx/mmCIF software resources [9]

_PDB entries deposited after July 20, 2027 will only be assigned 
extended PDB IDs and will follow a new DOI syntax._
On behalf of wwPDB,
Justin Flatt

Links:
------
[1] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2026*69ebcdca1103c56d3f444159__;Iw!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIl85KvkZ$ 
[2] https://urldefense.com/v3/__https://www.wwpdb.org/documentation/pdb-id-extension-faq__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIkeZxXo7$ 
[3] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-beta-ftp-sites__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIsD3uS5N$ 
[4] 
https://urldefense.com/v3/__https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner**Bs-guide-to-pdbx-mmcif__;4oCZ!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjItCPf-BG$ 
[5] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/user-guide/guide.html__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIrW7DWdc$ 
[6] https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIvHxDxrM$ 
[7] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIjx-_-yI$ 
[8] https://urldefense.com/v3/__https://pdbj.org/cif-editor/__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIlg6gVWG$ 
[9] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/software-resources.html__;!!Mih3wA!GFEBMqN4kUd02U1niyqMbOtZb5YSGK36Xp7fDWAHsQ6bc7PN_R2qh2axKYwB3-5gAgC7wwfQ6RpqqKnjIsUDWx6L$ 
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