PDB Deposition at EBI Macromolecular Structure Database

[Geoff Barton <geoff@ebi.ac.uk>]

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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
EBI.

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.

http://msd.ebi.ac.uk
mailto:msd@ebi.ac.uk

SUMMARY

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 
final processing. 

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
www.pdb.bnl.gov

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 
scripts
       "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 
RCSB.

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 
ftp.ebi.ac.uk/pub/databases/pdb/pub/resources/xdb_links/) from 
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 
structures.

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 
macromolecular structure.

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.

FEEDBACK

If you have questions arising from this announcement, please 
contact Geoff Barton, Head of EBI-MSD Project (geoff@ebi.ac.uk).

END OF ANNOUNCEMENT