Transition Plan

PLAN FOR THE TRANSITION OF THE PROTEIN DATA BANK (PDB) FROM BROOKHAVEN NATIONAL LABORATORY (BNL) TO THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS (RCSB)

Version 1.0

December 1, 1998

Prepared by the RCSB Project Team

An important goal for the coming year is to make the transition to the future PDB transparent. This detailed transition plan has being prepared by the RCSB at the request of the National Science Foundation (NSF). As changes approach, depositors and users will be notified in a variety of ways, including announcements on these pages. New components of the system will be introduced on a regular basis throughout the coming year.

We are looking forward to working with you in the years to come.

The RCSB Project Team

Helen M. Berman, John Westbrook, Rutgers University

Gary Gilliland, Phoebe Fagan, National Institute of Standards and Technology

Peter Arzberger, Phil Bourne, University of California, San Diego

1.0 DEPOSITION AND DATA PROCESSING

• Gradual phasing out of AUTODEP depositions.
• Staged deployment of new RCSB deposition tools for X-ray and NMR data.
• Processing of all entries at the Rutgers site starting January 27, 1999, and hence the cessation of the release of Layer 1 entries after January 27, 1999.
• Completion of final processing of all structures deposited before January 1999 by BNL. Entries "on hold" until dates after October 1999 will be put into final, ready-to-release form by BNL.
• Coordination of data deposition activities with sites at EBI and BMRB.

• Accept Layer 1 AUTODEP submissions from BNL and EBI sites starting January 27, 1999. Complete the data processing and annotation of entries prior to release. Completed files will be released within two weeks. Completed entries that are not on HOLD will be distributed by RCSB in PDB V2 format via ftp and the Web. CD-ROMs containing PDB V2 formatted files will be distributed by BNL. Files in the macromolecular Crystallographic Information File (mmCIF) format will be distributed by the RCSB via ftp and the Web.

• New deposition software for both X-ray and NMR data will be made available for testing. This tool is called ADIT (AUTODEP Input Tool). Laboratories interested in participating in the test program will be encouraged to use the new software and provide feedback during this beta test period, which will begin on January 27, 1999. The test period will extend until the system has been found to be robust by depositors and the archive. We expect this test period to last between two and four months. Following testing, ADIT will be made available for general use.
• Web accessible validation servers will be installed at each RCSB site. The validation server will accept coordinate and structure factor data and produce a report of geometrical and experimental checks. The content and presentation of the validation report is the same as the report that will be produced during the deposition process.

• Provide a tape copy of all on-line files systems associated with data deposition or data processing (received October 22, 1998).
• Provide for ongoing routine backup and archiving operations during the transition (under discussion).
• Provide initial statistics for structures in preparation, in processing, on hold or in queue (received October 15, 1998).
• Provide statistics on an on-going weekly basis of new structures deposited via AUTODEP (access to system provided October 19, 1998).
• Provide RCSB with documentation and technical descriptions for existing data processing procedures. This should include directions for finding all of the information about any deposition (data files, AUTODEP-generated files, depositor correspondence, manuscripts or preprints, corrections or revisions, or annotator notes; received October 29, 1998).
• Provide RCSB with access to AUTODEP software and any auxiliary software supporting data deposition, data processing, revision control, and archiving operations (received October 19, 1998).
• Provide RCSB with documentation for AUTODEP (received October 29, 1998).
• Provide RCSB with access to all data and software used for data deposition and processing operations (received October 22, 1998).

• Minimally modify existing AUTODEP deposition and data processing procedures at PDB to forward deposited data directly to the Rutgers site starting January 27, 1999 (Discussions are currently in progress).
• Continue to maintain AUTODEP throughout the transition period. No changes other than the correction of coding errors will be made. These changes will be reported to RCSB.
• New logins toAUTODEP will be turned off 45-60 days prior to October 1999.
• Corrections to final released entries will be forwarded by BNL to RCSB.
• For those structures in the queue, a monthly timetable for completing the processing of these entries during the transition period will be defined. A monthly progress report of the backlog structures processed will be provided. Processed structures and associated materials will be transferred to the Rutgers site for release.

• Gather information about all PDB data and software currently at BNL.
• Clarify data representation issues with EBI, BNL and BMRB for fields in current PDB files (in progress).
• Run annotator workshop for staff at Rutgers and NIST (Held October 15-16, 1998).
• Establish clear procedures for automatically forwarding data files from BNL to Rutgers (in progress).

November 1998

• Test processing of layer 1 for selected X-ray and NMR files deposited at BNL starting November 1, 1998. EBI and the National Center for Biotechnology Information (NCBI) will review the final files generated by the RCSB (in progress).
• Do alpha test of ADIT for X-ray and NMR data within RCSB group (in progress).
• Track data flow of incoming data to BNL required to establish workload and time schedule for RCSB assumption of BNL responsibilities (in progress).
• Recruit beta testers of ADIT from members of the international NMR and X-ray communities (in progress).
• Develop NMR Task Force guidelines and objectives. Define the combined requirements for a single RCSB/BMRB phase II ADIT for NMR (in progress).

• Make public announcement of the transition schedule.
• Establish expected workload and time schedule for processing structures in queue by BNL and new processing by RCSB. This will be based on statistics provided by BNL and by observation of the data flow by RCSB.
• Continue data processing of layer 1 depositions by RCSB.
• Complete draft of protocol for data exchange with EBI.
• Extend current ADIT for NMR by extending the underlying NMR dictionary. Draft protocol for exchange of data with BMRB.

• Beta testing of ADIT will begin.
• RCSB will begin discussions with new deposition centers in Japan and Israel.
• BNL will automatically forward all incoming data files to RCSB. RCSB will process all incoming files.
• RCSB will make validation server available for public use at all RCSB sites.
• RCSB will meet with EBI staff to review the draft protocol for data exchange.
• BNL will continue to work on all files in the queue as of January 27, 1999 with the goal of completing data processing of all these files by October 1999.

• RCSB will be responsible for all data processing with input coming from AUTODEP, ADIT and ASCII files.
• ADIT will be in final stages of testing and tuning. It will replace AUTODEP at some point during the transition period but no later than October 1999.
• BNL will continue to process all files in the queue as of January 27, 1999 and will continually forward these files to RCSB for distribution.

• The RCSB will become the primary distribution site for PDB data on February 3, 1999.
• The current BNL ftp structure will be maintained.
• A three-phase rollout of query capability accessible via the Web will be introduced.
• An RCSB ftp archive will be introduced in November 1998.
• New licensing agreements will be established with all class I and class II PDBSA contract holders.
• New RCSBmirrors will be established.
• The current modes of information dissemination (listserver, newsletter, Web documentation, and CD-ROM) will gradually shift from BNL to RCSB.
• BNL and the RCSB using the modes described above will report planned changes to service.

• Establish with the NSF the form and wording of the licensing agreements to be enacted by the RCSB.
• Notify the community of all impending changes well in advance of implementation.
• Accept data from Rutgers for public distribution as of January 27, 1999.
• Update new RCSB mirrors and other mirrors on weekly basis and as they come on-line.
• BNL will act as a mirror site as the data flow changes direction.
• Relocate the paper and the off-line media components of the PDB archive to NIST site.
• Start RCSB CD-ROM distribution in October 1999.
• Maintain periodic routine tape backups of all RCSB on-line facilities.
• Preserve quarterly tape backups of all RCSB on-line facilities.

• Continue to be responsible for BNL style mirrors that are currently in place until new contracts have been established and RCSB mirrors fully established.
• Provideall software and documentation associated with mirroring, 3DB browser, and PDB Lite (received October 22, 1998).
• Provide periodic snapshots of the complete PDB system (first received October 22, 1998).
• Provide contact information and state of development of mirrors in progress and any other mirrors not defined in the last PDB Newsletter (received October 16, 1998).
• Provide copies of all current PDBSA agreements, both class I and class II (received October 16, 1998).
• Provide current CD-ROM subscription list (complete demographic information) and notification of anyone requesting a subscription during the transition period (received October 16, 1998).
• Provide current list of subscribers to the PDB listserver and notification of new subscribers during the transition period (received October 16, 1998).
• Provide current list of subscribers to the PDB Newsletter both electronic (names and email addresses) and postal (full demographic information) (received October 16, 1998).
• Provide copies of all advisory notices ever signed (partial list for previous three years received October 22, 1998).
• Provide estimates of the type and organization of paper and off-line media in the current PDB archive (due October 29, 1998).

• Gather information as specified above from BNL (received).
• Invite members of the community as participants in a workshop to be held December 12, 1998 to discuss the development of the database resource (done).
• Recruit beta testers of the query interface from various niches of the user community (in progress).
• Implement mirrors at NIST and Rutgers (done).
• Obtain CD-ROM subscription list from BNL (received).
• Send tape copies of the current PDB site to the NIST site.

• Resolve licensing issues with NSF (in progress).
• Implement ftp site as ftp.rcsb.org (completed).
• Begin alpha testing of Phase I SearchLite (in progress).
• Draft mirror resource document.

• Notify PDBSA class I and II license holders of impending changes and begin new license agreements (to be effective February 1, 1999).
• Notify all mirror sites of potential changes from BNL to RCSB style mirrors.
• Hold Database Resource Development Workshop on December 12, 1998.
• Begin Phase I SearchLite beta testing.
• Complete mirror resource document.
• Test archival tape backup operations at the NIST site.

• Turn off gopher site at BNL.
• Release Phase I SearchLite.
• Begin Phase II alpha testing.
• Publish and distribute first RCSB newsletter.
• Notify all current PDB listserver subscribers of the new data flow and invite them to join the RCSB listserver.
• Obtain estimates of contents of archived paper and off-line computer media.
• Begin archival tape backup of the production RCSB site and of the Rutgers data and correspondence archive.
• Make plan for the installation of non-RCSB mirrors.

• Begin Phase II beta testing
• On-site inspection of archived hardcopy materials at PDB.

• Release Phase II query interface.
• Begin Phase III internal testing.
• Begin site preparation for archive materials at NIST.

• Publish plans for January 2000 CD-ROM distribution.
• First time stamped backup of RCSB preserved at NIST. Backups are preserved for each subsequent quarter.

• Create a test CD-ROM distribution for evaluation.

• Complete site preparations for archive at NIST.
• Do on-site preparation at BNL and organization of paper and off-line computer media and ship these materials to NIST.
• Create CD-ROM masters for January 2000 release.
• Tape copies of the PDB site at the end of the transition stored at the NIST site.