The wwPDB is planning to introduce in 2017 a new procedure for the
management by the Depositor of Record (where the Depositor of Record is
defined as the Principal Investigator for the entry) of substantial
revisions to previously released PDB archival entries.
At present, revised atomic coordinates for an existing released PDB
entry are assigned a new accession code, and the prior entry is
obsoleted. This long-standing wwPDB policy had the unintended
consequence of breaking connections with publications and usage of the
prior set of atomic coordinates, resulting in a non-trivial barrier to
submission of atomic coordinate revisions by our Depositors of Record.
The wwPDB is introducing a file versioning system that allows Depositors
of Record to update their own previously released entries. Please note,
in the first phase, file versioning will be applied to the atomic
coordinates refined versus unchanged experimental data.
Version numbers of each PDB archive entry will be designated using a #-#
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Thereafter, the major version digit is incremented with each substantial
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“Major version changes” are defined as updates to the atomic
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All other changes are defined as “minor changes”. When a major change is
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For the avoidance of doubt, the wwPDB will retain all major versions
with the latest minor versions of an entry within the PDB archive.
Current wwPDB policies governing the deposition of independently refined
structures based on the data generated by a research group or laboratory
separate from that of the Depositor of Record remain unchanged.
Versioning of atomic coordinates will be strictly limited to
substitutions made by the Depositor of Record.
Upon introduction of the file versioning system, the wwPDB will revise
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(e.g., "1abc" will become "pdb_00001abc"). This process will enable text
mining detection of PDB entries in the published literature and allow
for more informative and transparent delivery of revised data files. For
example, the atomic coordinates for the second major version of PDB
entry 1abc would have the following form under the new file-naming schema:
pdb_00001abc_xyz_v2-0.cif.gz
The wwPDB is mindful of the importance of continuity in providing
services and supporting User activities. For as long as practicable, the
wwPDB will continue assigning PDB codes that can be truncated losslessly
to the current four-character style. In the same spirit, initial
implementation of entry file versioning will appear in a new, parallel
branch of the PDB archive FTP tree. More details on the new FTP tree
organization and accessibility of version information will be
forthcoming. Data files in the current archive location
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the
familiar naming style and will contain the latest version in the
corresponding versioned archive.
<http://www.wwpdb.org/news/news?year=2017#top>
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: [email protected]
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
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