EMDB and beyond

1. EMDB and beyond CCP-EM community meeting 7 February 2013 ArdanPatwardhan and Gerard Kleywegt Protein Data Bank in Europe EMBL-EBI

2. Outline Introduction EMDB services Community consultations Plans pdbe.org

3. Literature and ontologies CiteXplore, UKPMC, (GO) Genomes EnsemblEnsembl Genomes EGA Protein sequences UniProt Protein families + motifs InterPro, Pfam Nucleotide sequence ENA Functional genomics ArrayExpress, Expression Atlas Molecular & cellular structure PDBe Protein expression PRIDE Interactions + pathways IntAct, Reactome Chemical entities ChEBI Chemogenomics ChEMBL Systems BioModels ebi.ac.uk

4. PDBe at a glance Mission: Bringing Structure to Biology Founding partner of Worldwide Protein Data Bank (wwPDB) Founder of Electron Microscopy Data Bank (EMDB) Major activities: • Deposition and annotation site for structural data on biomacromolecules (X-ray, NMR, EM) • Integrated resource to serve structural data and information • Liaise with structural biology community Guided by advisory bodies • PDBe, wwPDB, EMDataBank pdbe.org

5. Electron Microscopy Data Bank • Founded at EBI in 2002 • Since 2007 - operated jointly by PDBe and RCSB • NIH grant to NCMI + RCSB + PDBe (5 years) • RCSB as second deposition site • Integrate EMDB deposition with PDB (common tool) • Operate joint portal - EMDataBank.org • Policy harmonisation EMDB/PDB • Additional funding from BBSRC and EMBL-EBI • Own advisory board and validation task force • From 2013 - expecting renewal of NIH grant and supportfrom EMBL-EBI and EU (BioMedBridges)

6. EMDB holdings Tomography3% Electroncrystallography1% Helical9% Sub-tomogramaveraging9% Single particle78% 66 maps released in January! pdbe.org/emstats

7. EMDB services

8. Searching EMDB Advanced search: pdbe.org/emsearch Browse archive: pdbe.org/embrowse pdbe.org/emdb

9. Visualisation 3D viewer for all entries, e.g. pdbe.org/emd-2238/volume Slice viewer for tomograms, e.g. pdbe.org/emd-1906/slice

10. Analysis pages emd-2017, PDB: 4adv • Map/model overlays • Map/mask overlays • Atom-inclusion plots • FSC curves pdbe.org/emd-####/analysis

11. Community consultations

12. EM Validation Task Force, 2010 Recommendations on map validation, model validation and map/model validation Henderson et al., Structure 20, 205 (2012) DOI: 10.1016/j.str.2011.12.014

13. DMCEM, 2011 “Data-Management Challenges in3D Electron Microscopy” Recommendations: • Work with tomography community to encourage deposition • Set up a test-image repository • Develop and promote standardisation of file formats to capture richer content • Promote and encourage good practices w.r.t validation by providing web-based validation services Patwardhanet al., Nature SMB 19, 1203 (2012) DOI: 10.1038/nsmb.2426

14. 3DEM GRC, 2012 Special discussion session on tomography deposition Agreed on statement, circulated on 3DEM mailing list • Subtomogram-averaged reconstructions  mandatory deposition • Tomographic reconstructions  deposition of at least one representative tomogram strongly recommended • Overall positive response

15. 3DCC4MW, 2012 “3D Cellular Context for the Macromolecular World” New exciting cellular imaging techniques such as FIB/SEM and soft X-ray tomography Added value for general biologists when different scales of imaging/structure are linked together PDBe encouraged to: • Set up pilot archive for 3DSEM and SXT • Capture correlative LM in EMDB and pilot archives • Set up archiving facility for movies Meeting report to be published

16. Plans

17. New deposition and annotation system (D&A) Joint wwPDB project – same system to be used by all wwPDB partners Consistent interface for the deposition of EM/X-ray/NMR models and data: • Atomistic models, X-ray/NMR data PDB • EM/ET data, masks EMDB • (Additional NMR data BMRB) Better support for hybrid methods Value-added validation to be integrated with the system

18. EM validation services Promote and encourage good practices and consistency in reporting results FSC server will request relevant meta-data/data, calculate and display results, and create a file that can be uploaded into our deposition system Other ideas: • Tilt-pair validation server (from Peter Rosenthal’s lab) • Simulate SAXS profiles (and compare to actual data?) • Examine Euler-angle distribution/data completeness

19. Search service based on volume data BioMedBridges project – collaboration with STFC (Martyn Winn) Search for matches in database of shapes derived from PDB and EMDB Automated segmentation and fitting as EMDB/PDB grow Check fits that are deposited Align related structures http://www.biomedbridges.eu/workpackages/wp9

20. Pilot test-image repository Not very prescriptive to start with: micrographs, picked particles, and tilt series Minimal manual entry of meta-data • Link entries with EMDB • Harvest info from EPU, EMX, etc. Use Aspera for data transfer, OMERO for data presentation

21. Pilot 3DSEM and SXT archive Recommendation of 3DCC4MW meeting Use technology already used for other archives Data model needs to be adapted for 3DSEM and SXT Will require new funding

22. Movie archive linked to EMDB and PDB Develop using YouTube API Movies stored on YouTube Service to capture meta-data linking frames to entries

23. What do we hope to get from CCP-EM? Input on activities and plans Identifying use-cases Support in terms of data, and usage/testing of services Evaluation of software APIs and libraries needed to work with data and move it around

24. Questions & discussion