EMBL-EBI Data Archives – An Overview

The EMBL-EBI mission 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 Help disseminate cutting-edge technologies to industry Coordinate biological data provision throughout Europe

To enable life science research and its translation to medicine, agriculture, the bioindustries and society by providing biological data, information and knowledge EMBL-EBI Service Mission

What services do we provide? Labs around the world send us their data and we… Archive it Classify it Share it with other data providers Analyse it …provide tools to help researchers use it A virtuous circle

Some major service highlights

Web request distribution by country 2014

Challenges and opportunities Looking ahead

Structure going to EM 3D Molecular & Cellular Structure: PDB: >90,000 atomic structures, back to 1970s EMDB: ~2,000 maps and tomograms International collaborations Focus: Advanced services Chemical compounds Integration (structural data and bioinformatics data) Validation of data/models Experimental data

Shift to real time, in field, molecular measurement (DNA, RNA, Protein) (note: I am a long term paid consultant to Oxford Nanopore)

Research to Medical Research English as language Lightweight legal Identical/similar systems Open data Publications Grant-funding Practicing Medicine National language Heavy legal framework Very different systems Closed data Not published Contract-funding

Health Care systems NHS Single Payer “Single” organisation outside of GPs (eg, NICE payment rules) Commissioning moving to primary health care Standards by NICE Gesetzliche und private Krankenversicherungen Multiple payer Hospitals and independent GPs and consultants (Facharzt) Commissioning by insurance companies Standards by IQWiG

Bridges need at least two anchors

Long term goal There should be a Biomedical Informatics Institute in each Nation state Likely to be a network with a centre of gravity in larger countries We, along with Elixir nodes would interact with these Biomedical informatics institutes Transfering technology to them Providing reference datasets Receiving knowledge from clinical research

European and International Context

The challenge ahead of us… EMBL-EBI cannot scale to cover all of reference datasets needed over the next 10 years in molecular biology Technically – this is challenging, but feasible Scientifically and socially – this is the hardest thing to scale Clinical implementation demands National level engagement International reference datasets and schemes powerful but cannot be the “implementation” part

Elixir – the European Context EMBL-EBI Services are an Elixir Node, providing much of the backbone for Elixir

International Context Long term collaboration with NCBI and RCSB Over 30 years for DNA, over 20 years for wwPDB New NIH Extramural process: BD2K Funded participant on BD2K grants Collaborator with many BD2K centres Engagement with China, India, other countries More patchwork and nascent bioinformatics