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Update on PDB Data Deposition Specifications

Published byBritton Ross Modified over 9 years ago

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Presentation on theme: "Update on PDB Data Deposition Specifications"— Presentation transcript:

1 Update on PDB Data Deposition Specifications http://www.pdb.org/ info@rcsb.org

2 Defining SG Deposition Content Preliminary recommendations from the International Task Force on Deposition, Archiving, and Curation of Primary Information for Structural Genomics (Helen M. Berman & Geoff Barton, Chairs, and many participants) Extensions from the Working Group on Structural Genomics Data Deposition Significant participation from all Structural Genomics Projects Workshops

3 Task Force Members

4 Data Dictionary Working Group and Major Contributors Charles Weeks Hauptman-Woodward Institute (US) Rosalind Kim Berkeley Structural Genomics Center (US) John Westbrook PDB - Rutgers University (US) Eldon Ulrich BioMagResBank University Wisconsin (US) Cathy Lawson Rutgers University (US) John Ionides MSD-European Bioinformatics Institute (UK) Kim Henrick MSD- European Bioinformatics Institute (UK) Jonathan Diprose Oxford Protein Production Facility (UK) Paul Adams Lawrence Berkeley Labs (US)

5 Workshops Interdisciplinary Workshop promoting collaboration in high-throughput X-ray structure determination March 22-23, 2002, Santa Fe, New Mexico, USA Organizers: Tom Terwilliger, Paul Adams, Samar Hasnain Sponsor: Institute for Complex Adaptive Matter and the International Structural Genomics Organization Structural Genomics Informatics and Software Integration Workshop May 24-25, 2002, Hyatt Regency San Antonio Organizers: Helen M. Berman, Tom Terwilliger, John Westbrook Sponsors: National Institute of General Medical Sciences and International Structural Genomics Organization

6 Current Data Dictionaries http://deposit.pdb.org/mmcif/ PDB data exchange –Including structural genomics and data harvesting extensions mmCIF NMR Modeling Crystallization Symmetry Image data BIOSYNC

7 Dictionary Extensions for Structural Genomics Guiding Principles Data deposited will be at the level of journal “materials and methods” section Each data item must be carefully defined in PDB exchange data dictionary

8 X-ray Deposition Specifications Content includes: macromolecular naming, source organism, crystallization and cell parameters, data collection, structure solution and phasing, model building, refinement Significant additions beyond current PDB deposition content in data collection, phasing and model building Additional description of multi-method phasing experiments X-ray data items map closely to the output provided from existing structure determination applications and are easily extracted

9 NMR Specifications Content includes: macromolecular naming; source organism; sample description; experimental conditions and data collection; structure solution; constraints, force constants and related statistics; ensemble details and statistics Significant additions beyond current PDB deposition content in the details sample preparation, constraints, and all related statistics NMR data items map closely to the output provided from existing structure determination applications

10 Protein Production Specifications Content includes: target identification, source information, gene production, bacterial cloning, bacterial expression, purification Specifications attempt to integrate with existing LIMS Virtually all new content for deposition

11 Measurable Success Direct mmCIF depositions conforming to exchange dictionary fully annotated in 15 minutes

12 Next Steps X-ray –Dictionary ready for approval –PDB deposition specifications are well supported in applications –Extraction tools available to collect data items not exported in CIF –New multi-method phasing data items require testing NMR –Dictionary ready for approval –PDB deposition specifications are well supported in applications –Better direct support for NMRstar/NMRif and data extraction tools are needed Protein Production –Data dictionary drafted –Deposition specifications require testing and will need to be integrated with project LIMS

13 Access PDB Data Dictionaries and mmCIF Resource Site http://deposit.pdb.org/mmcif/ PDB TargetDB site http://targetdb.pdb.org/ PDB Structural Genomics Resource Page http://www.rcsb.org/pdb/strucgen.html PDB Software Download Site http://deposit.pdb.org/software/ mmCIF Beta Data Site ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmcif/ PDB Deposition Sites http://autodep.ebi.ac.uk/ http://pdbdep.protein.osaka-u.ac.jp/adit/ http://deposit.pdb.org/adit/

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