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John Westbrook Rutgers, The State University of New Jersey www.wwpdb.org The PDB and experimental data Workshop on Metadata for raw data from X-ray diffraction and other structural techniques

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Page 1: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

John Westbrook Rutgers, The State University of New Jersey

www.wwpdb.org

The PDB and experimental data

Workshop on Metadata for raw data from X-ray diffraction and other structural techniques

Page 2: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Overview

§  Current PDB audience and growth §  Range of PDB primary ‘experimental metadata’ §  Challenges for data acquisition and deposition

across the PDB view of the structural biology data pipeline

§  How we are addressing these challenges

Page 3: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Protein Data Bank (PDB) §  Single global repository for macromolecular

structure data (now >111K entries!)

§  Archival database - Users depend directly on the PDB; Other Databases present PDB contents

§  Our Users: Structural and Computational Specialists, Biophysicists, Biochemists, Biologists, Industrial Scientists, Educators, Students, and the General Public

Page 4: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Worldwide Protein Data Bank

§  Ensures data are freely available §  Data Centers

§  RCSB PDB (Research Collaboratory for Structural Bioinformatics)

§  PDBj (Osaka University) §  PDBe (EMBL-EBI) §  BioMagResBank (University

Wisconsin, Madison) §  Institutional agreement §  Formalized procedures for

deposition, validation, metadata representation, and annotation

§  Each data center provides unique delivery services

a  

Page 5: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

PDB  Depositors  >800  new  entries/month  

 

RCSB  PDB  347  million    

PDBe  100  million    

PDBj  58  million  

PDB  Users          FTP  and  RSYNC  Download  TrafDic  in  2014:  505  million  downloads    

Growing  Number  of        PDB  Depositions  

As  of  2014,  ~50%  increase  in  the  number  of  global  depositions  since  2008  

0  

2000  

4000  

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10000  

12000  

14000  

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2003  

2004  

2005  

2006  

2007  

2008  

2009  

2010  

2011  

2012  

2013  

2014  

2015  

2016  

2017  

2018  

Total  Number  of  Annual  Depositions  

Projected  Annual  Depositions  

Year  

#  of  Entries  

Archive Growth

Page 6: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Increasing Complexity

Number  of  entries  with  peptide-­‐like  inhibitors/antibiotics  released  per  year  

Year   Year  

#  of  Entries  

#  of  Entries  

Page 7: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Primary Experimental Content

…at the beginning of the

PDB pipeline

Page 8: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Sample Details •  Sample composition •  Chemical and molecular descriptions •  Source, production details, biological role •  Crystallization conditions •  Specimen preparation details

Page 9: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Data Collection Details

§  Instrumentation details §  Sample handling and collection conditions §  Data collection protocol

Page 10: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Skip a few steps …

Page 11: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Data Processing Steps

§  Summary statistics §  Software tools §  Processed data

Page 12: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Processed Data in the PDB Repository

§  Structure factor data sets for ~89% of current X-ray entries

§  ~10K additional data sets containing § Derivative and multiple wavelength data sets §  Intermediate phasing data § Map coefficients § Unmerged intensities

Page 13: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

PDB Data Acquisition

Model Easy Sample Harder

Go figure….

Page 14: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

New Deposition System

mmCIF/PDBx

End-to-end support for PDBx/mmCIF metadata

Page 15: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Data Harvesting Site pdb-extract.wwpdb.org/

Page 16: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Data Harvesting Site pdb-extract.wwpdb.org/

Page 17: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Structure Factor Utilities sf-tool.wwpdb.org/

Page 18: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Data Entry Forms

Minimize manual input using PDBx deposition format & PDB_EXTRACT

Page 19: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Chemical Assignment

Page 20: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Chemical Reference Data Chemical Component Dictionary

§  Library of all polymer and non-polymer chemical components in PDB §  >20,000 chemical component definitions §  400 additional definitions of amino acid

protonation variants §  ~700 new components released this year §  ~1700 component definitions updated this year §  Complimentary to the CCP4 monomer library

Page 21: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Using the experimental data we collect…

Page 22: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Leveraging Exp. Data in Quality Assessment

22

Gray – not modeled Green, yellow, orange, red – 0,1,2, 3 or more issues Red dot – poor fit to electron density

Page 23: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Map/Model Fit

Page 24: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Improving data acquisition …

Page 25: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

PDBx Deposition Working Group

PDBx Deposition Working Group Oct 8 2014 Workshop – EBI/Hinxton

wwPDB Deposition

PDBx Format in the Lab

Structure Determination

Pipeline

Round Trip

wwPDB Processing

and Annotation

PDBx Format in wwPDB ftp Archive

§  In 2011, charged with finding a “round trip” single format that can handle complex data not supported by the PDB file format

§  Consensus reached on using dictionary-driven PDBx format

§  Implementations delivered in January 2013 §  Currently working on recommendations for

delivery of non-standard chemistry and reflection/intensity data in later 2015

Page 26: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Recommendations Under Development

§  Improved organization and packaging of structure factor, intensity, phasing and map data

§  Controlled vocabulary of data set content types §  Standard specifications for each data category §  Improved linking between related data sets,

crystal samples, and refined models §  Incorporation of unmerged intensities and map

coefficients §  Comprehensive representation of chemical

topology and restraints

Page 27: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Restoring the missing bits …

Page 28: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Identifying Related Experimental Data

§  References to hosted data sets § DOIs for data sets § DOIs for related metadata §  Text descriptions of data and metadeta

Page 29: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

We Live in a Distributed World … just a few examples

http://www.ebi.ac.uk/pdbe/emdb/ http://www.ebi.ac.uk/pdbe/emdb/empiar/

http://www.sasbdb.org/

http://www.bmrb.wisc.edu/

http://proteindiffraction.org/

http://tardis.edu.au/deposit/

Page 30: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

First Step Data Identification - Next Step Federation

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop Structure 23: 1156–1167 doi: 10.1016/j.str.2015.05.013

Federation of loosely coupled resources with well defined data exchange protocols based on shared metadata standards.

Page 31: The PDB and experimental data - International Union of ...John Westbrook Rutgers, The State University of New Jersey The PDB and experimental data Workshop on Metadata for raw data

Acknowledgements

Funding: NIGMS


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