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PDB Deposition at EBI Macromolecular Structure Database
- To: firstname.lastname@example.org
- Subject: PDB Deposition at EBI Macromolecular Structure Database
- From: Geoff Barton <email@example.com>
- Date: Mon, 12 Apr 1999 10:51:29 +0100 (GMT Daylight Time)
- In-Reply-To: <Pine.WNT.firstname.lastname@example.org>
- Sender: email@example.com
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Apologies for the cross-posting of this message, but some may not have
seen this announcement. It concerns deposition and PDB services at the
30/March/1999: ANNOUNCEMENT FROM THE:
MACROMOLECULAR STRUCTURE DATABASE (EBI-MSD)
EUROPEAN MOLECULAR BIOLOGY LABORATORY OUTSTATION
EUROPEAN BIOINFORMATICS INSTITUTE
WELLCOME TRUST GENOME CAMPUS
HINXTON, CAMBRIDGE, CB10 1SD, UK.
The Research Collaboratory for Structural Bioinformatics (RCSB)
recently announced that as a result of co-operation between
Brookhaven National Laboratories (BNL) and RCSB staff, completion
of the smooth transition of Protein Data Bank (PDB) activities in
the USA from BNL to RCSB would be brought forward to 1 July 1999.
The transition from BNL to RCSB coincides with the EBI-MSD
assuming greater proportional responsibility for the management
of the world archive of data on macromolecular structure. This
process has been facilitated by EBI-MSD and RCSB forging a strong
collaboration over recent months. EBI-MSD anticipate that this
new collaboration will enable both groups to provide enhanced and
comparable services for producers and consumers of data on
macromolecular structure throughout the world, while ensuring the
continued integrity and uniformity of the PDB archive.
This announcement is primarily to explain how the PDB services
currently provided in Europe by the EBI-MSD will be managed and
improved through the transition. For background, a brief summary
of EBI-MSD goals and activities is given at the end of this
document. For further details, please see http://msd.ebi.ac.uk.
Information regarding the RCSB and further transition information
is available from http://www.rcsb.org.
DETAILS OF CURRENT ACTION
With completion of the transition from BNL to RCSB due at the end
of June 1999,the EBI-MSD will continue to maintain the following
services related to the PDB:
1. DEPOSITIONS via the BNL-AutoDep software at EBI (using
http://autodep.ebi.ac.uk/ ) will continue until Autumn 1999 when
AutoDep will be replaced by a new EBI-MSD deposition system.
Further details of the move to the EBI-MSD deposition system will
be announced in due course.
The Brookhaven National Laboratory (http://www.pdb.bnl.gov:8080/)
will stop running the AutoDep software for new submissions on May
31st 1999. The in-progress submissions at BNL will be accessible
until mid-June when all details will be transferred to the RCSB.
See the home page at all PDB mirror sites, e.g. at EBI
http://www2.ebi.ac.uk/pdb for information.
STARTING ON 1ST APRIL 1999 submissions at the EBI via
AutoDep(http://autodep.ebi.ac.uk/) will have the IDCode assigned
from the EBI within minutes of a completed submission, using the
current PDB policies for mandatory items and validation. The
submission data and files will be transferred to the RCSB for
STARTING ON 1ST JUNE 1999 submissions to the EBI-PDB AutoDep,
will be post-processed by EBI-MSD and all contact with depositors
for review questions will be carried out by the EBI-MSD. The
final PDB entry will then be passed to the RCSB for release to
the FTP sites via the ftp.rcsb.org site.
The RCSB ADIT deposition tool currently in beta test will be
available as an option at EBI. Support for ADIT submissions at
EBI will be provided by RCSB.
2. FTP access at the EBI (using ftp ftp.ebi.ac.uk )
The EBI-MSD will maintain the current BNL-PDB FTP structure and
continue to update this set of files by transferring the mirror
to give an exact copy of what were the files at ftp.pdb.bnl.gov
to an exact copy of the files held at bnlarchive.rcsb.org. The
FTP structure developed by RCSB will evolve over time and at an
appropriate point which will be announced, the EBI-MSD will
switch to a copy of the files held at ftp.rcsb.org.
3. 3DB browser and the EBI services of the BNL-PDB web-server
The current EBI copy of the service http://www.pdb.bnl.gov
available as http://www2.ebi.ac.uk/pdb will be maintained within
some limits. Some of the HTML pages will be replaced with RCSB
HTML documents, however, the cgi-bin services including the PDB
"opdbids opdbshort pdbids pdbmain save-pdb"
and the 3rd party scripts
"pdblite STING csu lpc"
will be maintained with locally produced index files.
The future of the ability to search the pending and on-hold lists
via the script "whsearch" will depend on details provided by
Each weekly release of new PDB entries requires a new set of
files for the www2.ebi.ac.uk/pdb service, these are only required
for the latest_release_date, the latest_entry_statistics, and the
LoadedID.html created each week. The EBI will create these files
independently of the RCSB/BNL-PDB.
The only external reference file totally dependent on PDB
processing required to make the new weekly indices will be the
med_line reference file. The continuing status of this file
medline.flat (from ftp
the RCSB, is still being finalised.
BACKGROUND TO EBI-MSD
The EBI-MSD project was established at the end of 1996 with
funding from the European Union and the UK Wellcome Trust to
create an autonomous European Centre for the deposition, archive
and distribution of information on macromolecular structures. We
have worked in collaboration with the BNL-PDB to establish
effective mirrors of the BNL-PDB site throughout the world and to
create at EBI the AutoDep deposition centre for data on
macromolecular structures. Since AutoDep started at EBI in
January 1998, we have taken more than 650 depositions to the PDB
and provided email support for depositors. In addition, we have
also contributed to the identification of key Mandatory Items
that should form part of every structural deposition, and to the
development of Validation Protocols for macromolecular
In August of 1998 the US funding agencies announced that the
award for PDB operations would transfer to the RCSB. A period of
phased transition of activities from BNL to the RCSB was begun in
October 1998 and will be completed in June, 1999. The MSD staff
at EBI have been working closely with our counterparts at the
RCSB since October on a number of issues regarding the present
transition and the future of the world archive of data on
Over the last 2.5 years, EBI-MSD project has performed a major
clean-up of PDB data. This includes the representation of
Quaternary Structures for macromolecules solved by X-ray
crystallography, protein sequences and cross-references to the
SWISS-PROT database, identification of 'To be published'
references and the classification of over 60,000 free text
remarks. This clean-up will be merged during 1999 with
complimentary work done at RCSB so as to enhance the quality and
usefulness of the PDB.
Access to some of the clean-up data and further information is
available from http://msd.ebi.ac.uk/.
In order to manage deposition, storage and dissemination of data
on macromolecular structure, the EBI-MSD project has been
developing database systems and protocols for deposition and
archive of the data. The new EBI deposition system which will be
in beta test in late summer, exploits advances in industry-
standard relational database technology. The EBI deposition
system draws on the philosophy of the BNL-AutoDep but enhanced by
modern database technology and application of our experience in
supporting depositions with AutoDep over the last 15 months.
If you have questions arising from this announcement, please
contact Geoff Barton, Head of EBI-MSD Project (firstname.lastname@example.org).
END OF ANNOUNCEMENT