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2nd Microscopy Congress: Public archiving of bio-imaging data - perspectives, chalenges and outlook
- 1. Public archiving of bio-imaging data – perspectives, challenges and outlook Ardan Patwardhan
- 2. Outline • Introduction • EMDB and EMPIAR status • Resources for EMDB and EMPIAR • On-going projects, initiatives and plans
- 3. Introduction
- 4. Molecular and Cellular Structure • Maintain and manage archives • PDB for atomic coordinate models • EMDB for 3DEM reconstructions • EMPIAR for 3DEM raw data • Develop and maintain web- services – searching, visualisation and validation • Facilitate community-wide initiatives • Key themes – integration with other bioinformatics resources and imaging scales and validation
- 5. Structural data archives Archive Type of data Founded Organization Funding # people # entries Size PDB Atomic coordinate models structures 1971 wwpdb (EBI, RCSB, PDBj, BMRB) Core + grants 60-80 124286 1 TB (8 MB) EMDB 3DEM volume structures 2002 EBI (+ RCSB, PDBj) Core + grants <10 4276 340 GB (80 MB) EMPIAR Raw image data for EMDB structures 2014 EBI grant <5 61 40 TB (660 GB) Stats until 9th Nov 2016
- 6. What goes where... • Final single-particle and sub-tomogram average maps must go to EMDB (tomograms strongly recommended) • Fitted models must go to PDB • Deposition of raw image data to EMPIAR is encouraged EMDBFinal map EMPIARRaw image data PDBFitted model
- 7. Benefits of public archiving • Reuse of data • starting models • compare structures of different functional states • different emphasis may lead to new discoveries • Validation, methods development, testing, training • Safe storage of data • Integration of data with other public archives • A resource for data mining • Enables a birds-eye perspective of the field
- 8. What does archiving involve? • Working with the community, partners and journals to achieve a consensus on practices, policies and procedures • Adapting to changing needs of data and meta-data collection • new sample preparation methods • new validation methods • Providing means to deposition data, e.g., web-based deposition systems • Curating data – automated + manual, remediation • maximize structured annotation, minimize free-text • Developing added value resources for searching, validating and visualizing data
- 9. Viability • Community support • Value – uploads versus downloads • Data transfer technologies – Aspera, Globus • Data storage – file systems, object stores • Data fidelity – quality measures and validation • Annotation – structured versus unstructured • Centralised versus distributed
- 10. EMPIAR • Electron microscopy pilot (or public?) image archive • Started in 2014 • Raw 2D image datasets related to EMDB • Usage: validation, development, testing, teaching and… • Safe storage of your data! • Was source for data in EM Map Validation Challenge • Multi-frame micrographs, averaged micrographs, particle- stacks, tilt series • Uses Aspera, Globus, ftp, http for data transfers
- 11. Websites • emdb-empiar.org – EMDB website • empiar.org – EMPIAR website • pdbe.org – PDBe website • wwpdb.org – Coordinating organization for pdb archive • emdatabank.org – EMDataBank NIH project website • https://www.facebook.com/proteindatabank • https://twitter.com/pdbeurope
- 12. EMDB and EMPIAR status
- 13. EMDB trends – released entries Stats until 2 Nov 2016 0 500 1000 1500 2000 2500 3000 3500 4000 4500 0 100 200 300 400 500 600 700 800 900 1000 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Cumulaveentries Releasedentriesperyear EMDB released entries trend Cumula ve entries Released entries per year
- 14. EMPIAR metrics • Number of entries: 61 (40TB; average size ~ 650GB) • 7 TB+ sets; one 10TB+ dataset • Transfer speed: uploads 1-2 TB/24h (Europe, US, Australia) • “empiar” cited 20+ times in full-text open-access papers • Nature Methods publication (Iudin et al., 2016) 0 1 2 3 4 2014 2015 2016 Aspera uploads/month (users) 0 0.5 1 1.5 2 2.5 3 2014 2015 2016 Aspera uploads/month (TB) 0 20 40 60 80 2014 2015 2016 Total downloads (users) 0 5 10 15 20 25 30 35 2014 2015 2016 Total downloads (data)
- 15. Resources for EMDB and EMPIAR
- 16. Searching EMDB - quick links + latest entries emdb-empiar.org
- 17. EMStats – journal stats
- 18. Volume slicer • Available for all EMDB entries • Published in J Struct Biol (Salavert Torres et al., 2016) emdb-empiar.org/emd-2363/3dslice
- 22. On-going projects, initiatives and plans
- 23. Volume browser • Integrated visualisation of structural data • Spanning scales from cells to molecules
- 24. Expert workshop on “3D segmentations and transformations - building bridges between cellular and molecular structural biology” Madingley Hall, 6-7 Dec 2015 Co-funded by
- 25. File format and translators • EMDB Segmentation File Format (EMDB-SFF) • adds structured biological annotation • handles transforms between tomograms and subtomograms • Python scripts to read Segger, IMOD and Amira and convert to EMDB-SFF • Working on displaying segmentations in Omero • Public open source distribution through CCP-EM
- 26. Future directions • Archiving for related imaging modalities including • 3D scanning electron microscopy • correlative light and electron microscopy • soft X-ray tomography • Data harvesting pipelines • Validation • Deposition support for new kinds of validation data • Validation servers, e.g., for visual analysis, map versus model FSC • Data-mining EMDB to develop new validation metrics • Fast archive-wide sub-structure volumetric (or shape-based) searches
- 27. Acknowledgements • Gerard Kleywegt • EM group • Sanja Abbott • Andrii Iudin • Paul Korir • Carlos Lugo • Eduardo Sanz Garcia • Jose Salavert Torres (UPV) • Ingvar Lagerstedt (EL) • Maya Holmdahl (UU) • Vladislav Lysenkov (MAMK) • Birkbeck • Maya Topf • Agnel Praveen Joseph • Helen Saibil • Baylor – Wah Chiu • RCSB – Cathy Lawson • Francis Crick • Lucy Collinson • Raffaella Carzaniga • STFC • Martyn Winn • Tom Burnley • Dundee • Jason Swedlow • Josh Moore • CNB Madrid • Jose Maria Carazo • Pablo Conesa • Jose Miguel de la Rosa Trevin • Joan Segura Mora • And many more!
Editor's Notes
- (*) Biological annotation added by hand