EMBL-EBIEMBL-EBI EMBL-EBI 2006

EMBL-EBIEMBL-EBI

What is the EBI's particular niche?

• Provides Core Biomolecular Resources in Europe – Nucleotide; genome, protein sequences, structures,

expression data, proteomics, pathways …. • EBI represents Europe in international database consortia• Develops shared standards and ontologies • Provides Interconnectivity – uniquely EBI holds all the core

biomolecular resources in one institute• Complements Model Organism data resources and provide

standards for or links to other genome/proteome data• Provides a central hub to facilitate future ‘coordination’ of

Smaller Related Biomolecular Data Resources in Europe and links to other data resources in related disciplines

• Provides a unique environment for research and training

Databases: molecules to systems

GenomesEnsembl, Integr8

GenomesEnsembl, Integr8

Nucleotide sequenceEMBL-Bank

Nucleotide sequenceEMBL-Bank

Gene expressionArrayExpress

Gene expressionArrayExpress

Protein sequenceUniProt

Protein sequenceUniProt

Protein families, motifs and domains

InterPro

Protein families, motifs and domains

InterPro

Protein structureMSD

Protein structureMSD

Protein interactionsIntAct

Protein interactionsIntAct

Chemical entitiesChEBI

Chemical entitiesChEBI

PathwaysReactome

PathwaysReactome

SystemsBioModels

SystemsBioModels

Research groups: Molecules to Systems

HuberFunctional genomics

HuberFunctional genomics

Rebholz-SchuhmannText mining

Rebholz-SchuhmannText mining

ThorntonStructural bioinformatics

ThorntonStructural bioinformatics

GoldmanEvolutionary sequence analysis

GoldmanEvolutionary sequence analysis

LuscombeRegulatory networks

LuscombeRegulatory networks

Le NovèreComputational systems

neurobiology

Le NovèreComputational systems

neurobiology

BertoneRegulation

BertoneRegulation

At EBI the majority of our staff work to provide data services

Data Services

71%

Research

19%

Systems 4% Admin 6%

Current Total EMBL-EBI Staff ~ 300

Data Resources @ EBI

Intact

InterPro

EMBL

Ensembl

ArrayExpress

MSD UniProt Reactome

Staff Commitment to Different Data Resources @ EBI

0100002000030000400005000060000700008000090000

100000

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

0

5000

10000

15000

20000

25000

30000

35000

EMBL-Bank1982-2005

UniProt etc.1986-2005

MSD1972-2005

Me

ga

base

s

En

trie

s

En

trie

s

All EBI’s Data Resources are growing rapidly

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

1st99

2nd99

3rd99

4th99

1st00

2nd00

3rd00

4th00

1st01

2nd01

3rd01

4th01

1st02

2nd02

3rd02

4th02

1st03

2nd03

3rd03

4th03

1st04

2nd04

3rd04

4th04

1st05

2nd05

3rd05

Average Web Hits per Day

Including Ensembl

Quarter Year

Ave

rage

Hits

per

Day

Note: Ensembl is a joint project withThe Wellcome Trust Sanger Institute. Equivalent usage data have only beenavailable since 2004.

A few hundred thousandunique users per month

A million unique usersper year

EBI

How do we cope with this deluge of data?

By sharing the task and using new (GRID) technologies

All the Core Databases are part of international collaborations – exchanging data freely

EMBL-EBIEMBL-EBI

EBI

RCSB PDBJ

Database CollaborationsUniProtEBI & SIB & PIR

INSDCEMBL/Genbank/DDBJ

EBI SIB

EBI

NCBI DDBJJ

wwPDBMSD/RCSB/PDBJ

PDBPIR

Ensembl – EBI & SangerReactome – EBI & CSHL

InterPro: (10 partners) Protein FamiliesImex: (5 Partners) Protein-protein Interactions

Good Collaborations are difficult to achieve and maintain!

EMBL-EBIEMBL-EBI

Members of a Consortium share tasks, where possible

• UniProt – EBI/SIB/PIR– SIB – All plant annotation; literature; Annotation

platform– EBI – All GO annotations; higher eukaryote

annotation; software development; TREMBL– PIR – UniRef Reference sequences

• wwPDB – RCSB/EBI/PDBj – e.g. in legacy Clean-up

• RCSB - ligands• EBI - Sequences, taxonomy, entities• PDBj - Literature

EMBL-EBIEMBL-EBI

International Data Collection

EBI process ~16% of Structures: 30% increase in last year

EBI process ~15% of nucleotides globally

13% increase in curated entries in last year (700 sequences /day)

EBI process ~40% deposited data

270% Increase in last year

Collaborations

Joint publications

Joint grants

EBI helps to Promote Bioinformatics in Europe

• Coordination of EU Networks of excellence– BioSapiens – Support for bioinformatics

research to generate ‘Distributed genome Annotation’

– EMBRACE – technical integration of tools – web services

– Enfin – Experimental network for Functional Integration

€ 0

€ 10

€ 20

€ 30

€ 40

€ 50

€ 60

NCBI 2004/5 + PDB EBI 2005 EBI 2011

Mill

ions

Funding also helps!!

Training Programme 2005

Training – Main Focus is on user-training

User training – 67 workshops, including touring workshops

Development of EBI Training web site

Through European Networks of Excellence, coordinated by EBI (BioSapiens & EMBRACE) we provide organisation for virtual Training Institute

EBI also provides the usual EMBL-wide training activitiesPhD students, post-docs, Marie-Curie students, plus

trained professional bioinformatics software engineers

EnsEMBLGenome

Annotation

EMBL-BankDNA sequences

UniProtProtein Sequences

Array-ExpressMicroarray

Expression Data

EMSDMacromolecularStructure Data

IntActProtein Interactions

Reactome

DATA INTEGRATION

InterPro

EMBL-EBIEMBL-EBI

EMBL-EBIEMBL-EBIWho uses EBI resources?

Response to User Survey (656 responses in total to date)

0 50 100 150 200 250 300 350

Agriculture

Medicine

Neurobiology

Maths

Developmental Biology

Immunology

Other

Computer Science

Cell Biology

Biotechnology

Genetics

Biochemistry

Molecular Biology

Bioinformatics

Number of responses

EBI User Forum ISMB Tuesday 12.30pm

Flybase

MGD

SGD

BRENDA

Chemicaldata

resources

Medical data resources

Biodiversitydata

resources

IMGT

Pasteur DBs

Eumorphia/Phenotypes

Corebiomolecular

resources

Specialist biomolecular data resource examples

Mutants

Large resources in related disciplines

Model organism resource examples

Mouse Atlas

Expansion of EMBL-EBI

After detailed scientific scrutiny, the EMBL Scientific Advisory Committee approved an expansion of EBI to ~ 400 staff

In Dec 2005 funding was secured for a building extension to permit this expansion

€ 0

€ 10

€ 20

€ 30

€ 40

€ 50

€ 60

NCBI 2004/5 + PDB EBI 2005 EBI 2011

Mill

ions

Funds for running costs still under discussion

Funds for running costs still under discussion

MSD Advisory Board 16/17 Feb, 2006

Current EBI

New Wing

Plans For

EBI

Extension

Funded by

Wellcome Trust,

UK MRC & BBSRC

& EMBL

EBI New Wing – Topping out Ceremony July 2006

Come and Visit EBI at HinxtonCome and Visit EBI at Hinxton

http://www.ebi.ac.ukhttp://www.ebi.ac.uk