EMBL-EBI EMBL-EBI 2006

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

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

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

Staff Commitment to Different Data EBI

EMBL-Bank UniProt etc MSD Megabases Entries All EBI’s Data Resources are growing rapidly

Average Web Hits per Day Including Ensembl Quarter Year Average Hits per Day Note: Ensembl is a joint project with The Wellcome Trust Sanger Institute. Equivalent usage data have only been available since A few hundred thousand unique users per month A million unique users per 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-EBI EBI RCSB PDB J Database Collaborations UniProt EBI & SIB & PIR INSDC EMBL/Genbank/DDBJ EBI SIB EBI NCBI DDBJ J wwPDB MSD/RCSB/PDB J PDB PIR Ensembl – EBI & Sanger Reactome – EBI & CSHL InterPro: (10 partners) Protein Families Imex: (5 Partners) Protein-protein Interactions

Good Collaborations are difficult to achieve and maintain! EMBL-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-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

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 activities  PhD students, post-docs, Marie-Curie students, plus trained professional bioinformatics software engineers

EnsEMBL Genome Annotation EMBL-Bank DNA sequences UniProt Protein Sequences Array-Express Microarray Expression Data EMSD Macromolecular Structure Data IntAct Protein Interactions Reactome DATA INTEGRATION InterPro

EMBL-EBI

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

Flybase MGD SGD BRENDA Chemical data resources Medical data resources Biodiversity data resources IMGT Pasteur DBs Eumorphia/ Phenotypes Core biomolecular 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 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 Hinxton