EMBL-EBI: Data resources and services

Katrina Pavelin Scientific Engagement Officer EMBL-EBI [email protected] About me

• My role is to promote EMBL-EBI to scientific audiences • Please help yourself to our Guide to Resources and EBI in a Nutshell brochure – and a love data postcard! • I will be taking photographs here. • The videos of the talks will appear in Train online, and there will be a short article and photographs on our SME web pages.

EMBL-EBI What is the European Bioinformatics Institute?

• Non-profit research institute • Provider of freely available bioinformatics services • Part of the European Molecular Biology Laboratory (EMBL) • Based on the Wellcome Trust Genome Campus with WTSI

EMBL-EBI EMBL member states

Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom

Associate member state: Australia

EMBL-EBI EMBL-EBI also has significant external funding Sources of external funding for the year 2011. The Wellcome Trust also supports us through provision of our buildings.

The UK government granted £75 million in 2011 to support our role in coordinating ELIXIR, the emerging infrastructure for biological data in Europe.

EMBL-EBI The five branches of EMBL

Heidelberg Hamburg Hinxton

• Basic research in Structural biology Bioinformatics molecular biology • Administration Grenoble Monterotondo • EMBO

• >1500 staff • >60 nationalities Structural biology Mouse biology

EMBL-EBI What does EMBL-EBI do?

• Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Disseminate cutting-edge technologies to industry • Coordinate biological data provision across Europe

EMBL-EBI The people behind the data and research

~550 staff ~400 in services & support

>45 nationalities ~100 in research

EMBL-EBI Staff nationalities

Nationalities of EMBL-EBI members of personnel as of December 2011

EMBL-EBI Services www.ebi.ac.uk/services

EMBL-EBI Key facts about EBI services

• Freely available • The world’s most comprehensive collection of molecular databases • Globally coordinated data collection and dissemination • Produced in collaboration with other world leaders, e.g. • NCBI, USA • National Institute of Genetics, Japan • Swiss Institute of Bioinformatics (SIB) • Cold Spring Harbor Laboratory, USA

EMBL-EBI Databases: molecules to systems Literature and ontologies • UKPMC, CiteXplore, GO Genomes • Ensembl • Ensembl Genomes Protein families, • EGA motifs and domains • Metagenomics • InterPro portal Functional genomics • ArrayExpress Macromolecular • Expression Atlas Nucleotide sequence structure • ENA • PDBe

Pathways Protein activity • Reactome • IntAct, PRIDE • Metabolites

Protein Sequences • UniProt

Systems Chemical entities Chemogenomics • ChEBI • BioModels • ChEMBL • BioSamples

EMBL-EBI Data management

• Over 5M web requests per Growth of raw storage day – over 5.7M if Ensembl at EMBL-EBI (in terabytes) is included • Total disk space: 14 16000 petabytes in 2011 14000 12000

• Leased two data centres 10000

(with €11.4M from UK 8000

Research Councils) 6000 Disks (TB) Disks • Over 800 million cross- 4000 references in the 2000 databases we serve 0

Year

EMBL-EBI Search EMBL-EBI’s data

Access from the EBI’s homepage

Species selector allows for easy comparison

Data organised according to: • gene • expression Explore data, • protein return easily to • structure your results • literature

EMBL-EBI Research www.ebi.ac.uk/groups

EMBL-EBI Key facts about research at EMBL-EBI

• A unique environment for bioinformatics research • Dedicated research groups • Services teams also carry out R&D • Research and services are mutually supportive

EMBL-EBI Research themes

Genomes Nick Goldman Proteins Oliver Stegle Janet Thornton Ewan Birney Rolf Apweiler Paul Flicek Gerard Kleywegt

Transcriptomes Anton Enright Chemistry John Marioni Christoph Steinbeck Alvis Brazma John Overington

Pathways and systems Service team leaders Paul Bertone who also have Julio Saez-Rodriguez research groups are Pedro Beltrau in italics

EMBL-EBI SME support www.ebi.ac.uk/industry/sme

EMBL-EBI Small and medium-sized enterprises

• SMEs are major drivers of the economy

• Turnover is high: needs are often more short-term

• EMBL-EBI data and services can add value to business processes Attendees of the 2011 SME Forum in Piemonte, Italy immediately

EMBL-EBI SME Forum

• Annual SME workshop

• Different location in Europe every year

• Regionally co-funded

• Topics chosen with input 2011 SME Forum co-host Fabrizio from regional focus group Conicella of BioPmed

EMBL-EBI Training www.ebi.ac.uk/training

EMBL-EBI • Coordinated centrally through EMBL Heidelberg

• PhDs awarded from the University of Cambridge

www.embl.org/phdprogramme

www.embl.org/phdprogramme EMBL-EBI Postdocs at EMBL-EBI

EIPOD: EMBL-sponsored ESPOD: EBI–Sanger combined interdisciplinary fellowships experimental and computational fellowships

EMBL-EBI 2 EMBL-EBI 4 Coordinating bioinformatics in Europe

EMBL-EBI ELIXIR

• Sustainable research infrastructure for Europe’s biological databases

• Safeguard the funding

• Widely adopted standards will reduce barriers between information sharing and help facilitate cross-company research partnerships.

www.elixir-europe.org

EMBL-EBI

Signatories to the ELIXIR Memorandum of Understanding

EMBL-EBI Thank you! Any questions?

EMBL-EBI