the european molecular biology laboratory (embl) is supported by sixteen countries

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

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

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

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

Genomes

Hypotheses andin silico models

Bioinformatics

Expression-profiling

Comparativegenomics

Mutant/RNAidata

Metabolic data

Literature

Proteome data

Biochemistry

Molecules to Cells to Organisms

E.coli GenomeProtein

Genomes

Systems BiologySystems Biology

Output

Input

CheZ

CheWCheWCheB ATP

ADPPi

Methyl

CheR

MethylAdaptorAdaptor

Flim C

PiCheY

CheA

Molecular Basis of Disease

p53 tumour suppressor core domain – cancers of many types

Cu-Zn SuperoxideDismutase - Autosomal dominantAmyotrophic lateral sclerosis

From Structure to Functional Annotation

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

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?

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

Data Growth

Web requests per day(excluding Ensembl)

ftpyear million files; Terabytes2001 4.5 119142002 5.6 118092003 13.5 438602004 17.3 605082005 26.3 85396

Web Servers Requests millions

2002 118631650 118 2003 255399724 2552004 354235704 3542005 482076196 482

Distinct hosts served Number users(millions)2002 1586883 1.52003 2784974 2.72004 3656109 3.62005 3919564 3.9

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%

The Services of the EBI

Nucleotide sequences Genes Transcription information Protein sequences Protein families Macromolecular structures Molecular interactions Pathways Metabolic information Scientific Literature

Structure of EBI: Services

Structure of EBI: Services

Apweiler,Stoesser

Brazma

Birney

Henrick

Database Integration and External Services Lopez

Stoehr, Zhu

Structure of EBI: Research

Structure of EBI: Research

Text Mining Computational Genomics

Structural Proteomics

Neuroinformatics

Phylogeny & Evolution

EBI DATA BASES

EMBL-BankDNA sequences

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

Protein Sequences

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

Protein Sequences

EMSDMacromolecularStructure Data

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

Protein Sequences

Array-ExpressMicroarray

Expression Data

EMSDMacromolecularStructure Data

EnsEMBLHuman GenomeGene Annotation

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

Protein Sequences

Array-ExpressMicroarray

Expression Data

EMSDMacromolecularStructure Data

EnsEMBLHuman GenomeGene Annotation

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

Protein Sequences

Array-ExpressMicroarray

Expression Data

EMSDMacromolecularStructure Data

IntActProtein Interactions

GKBPathways

EnsEMBLHuman GenomeGene Annotation

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

Protein Sequences

Array-ExpressMicroarray

Expression Data

EMSDMacromolecularStructure Data

IntActProtein Interactions

Integration

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

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

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

Industry Support

Industry Support

Current successful Industry programme for Pharma Quarterly meetings R&D Training - workshops Industry Forum Funded by subscriptions

New SME programme under development

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/

The Magic Search Box