emdb and beyond
DESCRIPTION
EMDB and beyond. CCP-EM community meeting 7 February 2013. Ardan Patwardhan and Gerard Kleywegt Protein Data Bank in Europe EMBL-EBI. Outline. Introduction EMDB services Community consultations Plans. pdbe.org. Literature and ontologies CiteXplore , UKPMC, (GO). Genomes - PowerPoint PPT PresentationTRANSCRIPT
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CCP-EM community meeting7 February 2013
EMDB and beyond
Ardan Patwardhan and Gerard KleywegtProtein Data Bank in EuropeEMBL-EBI
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Outline• Introduction • EMDB services• Community consultations• Plans
pdbe.org
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ebi.ac.uk
GenomesEnsembl
Ensembl Genomes EGA
Nucleotide sequenceENA Functional genomics
ArrayExpress, Expression Atlas
Protein sequencesUniProt
Protein families + motifs InterPro, Pfam
Molecular &cellular structure
PDBeProtein expression
PRIDE
Chemical entitiesChEBI
Interactions + pathways
IntAct, Reactome
Literature and ontologiesCiteXplore, UKPMC, (GO)
ChemogenomicsChEMBL
SystemsBioModels
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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, EMDataBankpdbe.org
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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)
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EMDB holdings
pdbe.org/emstats
Single particle78%
Sub-tomogramaveraging
9%
Helical9%
Tomography3% Electron
crystallography1%
66 maps released in January!
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EMDB services
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Searching EMDB• Advanced search: pdbe.org/emsearch• Browse archive: pdbe.org/embrowse
pdbe.org/emdb
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Visualisation• 3D viewer for all entries, e.g.
pdbe.org/emd-2238/volume• Slice viewer for tomograms, e.g. pdbe.org/emd-
1906/slice
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Analysis pages• Map/model overlays• Map/mask overlays• Atom-inclusion plots• FSC curves
pdbe.org/emd-####/analysis
emd-2017, PDB: 4adv
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Community consultations
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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
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DMCEM, 2011• “Data-Management Challenges in
3D 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• Patwardhan et al., Nature SMB 19, 1203 (2012)
DOI: 10.1038/nsmb.2426
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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
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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
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Plans
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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
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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
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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
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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
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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
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Movie archive linked to EMDB and PDB• Develop using YouTube API• Movies stored on YouTube• Service to capture meta-data linking frames to
entries
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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
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Questions & discussion