EMBL-EBI 2006

1. EMBL-EBI 2006

2. 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

3. Databases: molecules to systems Nucleotide sequence EMBL-Bank Genomes Ensembl, Integr8 Protein sequence UniProt Gene expression ArrayExpress Protein structure MSD Protein families, motifs and domains InterPro Chemical entities ChEBI Protein interactions IntAct Pathways Reactome Systems BioModels

4. Research groups: Molecules to Systems Rebholz-Schuhmann Text mining Goldman Evolutionary sequence analysis Huber Functional genomics Bertone Regulation Thornton Structural bioinformatics Luscombe Regulatory networks Le Novère Computational systems neurobiology

5. At EBI the majority of our staff work to provide data services Current Total EMBL-EBI Staff ~ 300 Systems 4% Admin 6% Research 19% Data Services 71%

6. Staff Commitment to Different Data Resources @ EBI

7. EMBL-Bank 1982-2005 UniProt etc. 1986-2005 Entries Megabases MSD 1972-2005 Entries All EBI’s Data Resources are growing rapidly

8. Average Web Hits per Day Including Ensembl A few hundred thousand unique users per month Average Hits per Day A million unique users per year Note: Ensembl is a joint project with The Wellcome Trust Sanger Institute. Equivalent usage data have only been available since 2004. Quarter Year

9. EBI

10. How do we cope with this deluge of data? By sharing the task and using new (GRID) technologies

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

12. EBI PDBJ RCSB Database Collaborations UniProt EBI & SIB & PIR wwPDB MSD/RCSB/PDBJ SIB EBI PDB PIR EBI INSDC EMBL/Genbank/DDBJ Ensembl – EBI & Sanger Reactome – EBI & CSHL InterPro: (10 partners) Protein Families Imex: (5 Partners) Protein-protein Interactions DDBJJ NCBI

13. Good Collaborations are difficult to achieve and maintain! EMBL-EBI

14. 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

15. International Data Collection EBI process ~15% of nucleotides globally 13% increase in curated entries in last year (700 sequences /day) EBI process ~16% of Structures: 30% increase in last year EBI process ~40% deposited data 270% Increase in last year

16. Collaborations Joint publications Joint grants

17. 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

18. Funding also helps!!

19. 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 activities • PhD students, post-docs, Marie-Curie students, plus trained professional bioinformatics software engineers

20. DATA INTEGRATION Reactome EMBL-BankDNA sequences Array-Express Microarray Expression Data UniProt Protein Sequences EnsEMBL Genome Annotation IntActProtein Interactions InterPro EMSD Macromolecular Structure Data

22. Who uses EBI resources?Response to User Survey (656 responses in total to date) EBI User Forum ISMB Tuesday 12.30pm

23. Large resources in related disciplines BRENDA IMGT Pasteur DBs Model organism resource examples Specialist biomolecular data resource examples Medical data resources Core biomolecular resources Biodiversity data resources SGD Flybase Chemical data resources MGD Eumorphia/ Phenotypes Mutants Mouse Atlas

24. 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 Funds for running costs still under discussion

25. Funded by Wellcome Trust, UK MRC & BBSRC & EMBL Plans For EBI Extension New Wing Current EBI

26. EBI New Wing – Topping out Ceremony July 2006

27. Come and Visit EBI at Hinxton http://www.ebi.ac.uk