The European Molecular Biology Laboratory (EMBL) is supported by sixteen countries.
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Transcript of The European Molecular Biology Laboratory (EMBL) is supported by sixteen countries.
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The European Molecular Biology Laboratory (EMBL) is supported by sixteen countries.
Consists of the main Laboratory in Heidelberg (Germany), Outstations in Hamburg (Germany), Grenoble (France) and Hinxton (U. K.), and an external Research Programme in Monterotondo (Italy).
http://www.embl.de/
from 1974
http://www.ebi.ac.uk/
from 1996
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The EBI Mission
To provide Bioinformatics Facilities for the Scientific Community
To become a flagship laboratory for research in bioinformatics
To provide bioinformatics training To help disseminate standards &
technologies
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Role of Bioinformatics
To Support Experimental BiologyTo Collect and Archive DataTo provide Framework and IntegrationTo give Easy Access to Data
To make New Discoveries through Data Analysis
To predict through modelling To facilitate application and exploitation of
academic research in Medicine, Agriculture, Health and Environment
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Dramatic Changes in Biology over last 5 years
Data Explosion & New Types of Data Move towards High-Throughput Biology Move towards Systems Biology Much larger community – often naïve users Growth of Applied Biology – molecular
medicine, agriculture, food, environmental sciences
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Genomes
Hypotheses andin silico models
Bioinformatics
Expression-profiling
Comparativegenomics
Mutant/RNAidata
Metabolic data
Literature
Proteome data
Biochemistry
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Molecules to Cells to Organisms
E.coli GenomeProtein
Genomes
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Systems BiologySystems Biology
Output
Input
CheZ
CheWCheWCheB ATP
ADPPi
Methyl
CheR
MethylAdaptorAdaptor
Flim C
PiCheY
CheA
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Molecular Basis of Disease
p53 tumour suppressor core domain – cancers of many types
Cu-Zn SuperoxideDismutase - Autosomal dominantAmyotrophic lateral sclerosis
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From Structure to Functional Annotation
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PQS biological assemblies
MSDchem ligand data
Electron Density VisualisationAstexViewer MSDPro, MSDlite
SSM fold matching Surface MatchingMSDsite Active sites
Linking to Domain data, eFamily
Sequence Mapping, SIFTS
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From Structure To Biochemical Function
Gene Protein 3D Structure Function
Given a protein structure: Where is the functional site? What is the multimeric state of the protein? Which ligands bind to the protein? What is biochemical function?
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High throughput
A new sequence every 4 seconds 600 000 web requests a day 100 000 users 5-10 core databases 20 000 000 cross-references About 160 other databases
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Data Growth
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Web requests per day(excluding Ensembl)
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ftpyear million files; Terabytes2001 4.5 119142002 5.6 118092003 13.5 438602004 17.3 605082005 26.3 85396
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Web Servers Requests millions
2002 118631650 118 2003 255399724 2552004 354235704 3542005 482076196 482
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Distinct hosts served Number users(millions)2002 1586883 1.52003 2784974 2.72004 3656109 3.62005 3919564 3.9
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dynamic pages domains (2005)
1. .uk (United Kingdom) 21.14% 2. .com (Commercial) 17.16% 3. [unknown domain] 13.37% 4. [unresolved numerical addresses] 11.05% 5. .edu (USA Higher Education) 5.29% 6. .net (Networks) 5.27% 7. .fr (France) 4.76% 8. .it (Italy) 4.68% 9. .de (Germany) 2.81% 10. .nl (Netherlands) 2.00%
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The Services of the EBI
Nucleotide sequences Genes Transcription information Protein sequences Protein families Macromolecular structures Molecular interactions Pathways Metabolic information Scientific Literature
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Structure of EBI: Services
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Structure of EBI: Services
Apweiler,Stoesser
Brazma
Birney
Henrick
Database Integration and External Services Lopez
Stoehr, Zhu
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Structure of EBI: Research
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Structure of EBI: Research
Text Mining Computational Genomics
Structural Proteomics
Neuroinformatics
Phylogeny & Evolution
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EBI DATA BASES
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EMBL-BankDNA sequences
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EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
Protein Sequences
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EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
Protein Sequences
EMSDMacromolecularStructure Data
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EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
Protein Sequences
Array-ExpressMicroarray
Expression Data
EMSDMacromolecularStructure Data
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EnsEMBLHuman GenomeGene Annotation
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
Protein Sequences
Array-ExpressMicroarray
Expression Data
EMSDMacromolecularStructure Data
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EnsEMBLHuman GenomeGene Annotation
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
Protein Sequences
Array-ExpressMicroarray
Expression Data
EMSDMacromolecularStructure Data
IntActProtein Interactions
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GKBPathways
EnsEMBLHuman GenomeGene Annotation
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
Protein Sequences
Array-ExpressMicroarray
Expression Data
EMSDMacromolecularStructure Data
IntActProtein Interactions
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Integration
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Integrative science demandsintegrative resources
EBI databases have a backbone of integrative links
20 000 000 cross-references support trans-database navigation
Is this good enough? sparse and coarse-grain not straight-forward to use
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Integrative science demands
integrative resources
Major efforts involved in integration Interpro: database of protein families, domains and functional sites. Interg8: data integration project co-ordinated by the EBI, to provide an integrated layer for the exploitation of genomic and proteomic data. GRID technologies
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European Patent Office
Support the inclusion of sequence data in the public databases
Development of tools to capture sequence data
Run their searches at the EBI (similar arrangements in USA and Japan
ensure exchange) Analogous systems being developed for
structure information
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Industry Support
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Industry Support
Current successful Industry programme for Pharma Quarterly meetings R&D Training - workshops Industry Forum Funded by subscriptions
New SME programme under development
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New Data
Expression Data
Proteomic Data
Metabolome Data
Chip-on-Chip
Atlases
Electron tomographs
Human Variation
Disease Links
??
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http://www.ebi.ac.uk/2can/
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The Magic Search Box
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