embl-ebi embl-ebi 2006. embl-ebi what is the ebi's particular niche? provides core biomolecular...
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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
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
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
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-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