A European Infrastructure for Biological Information

1. Genome Protein Cell Embryo Fruitfly Mouse Human Development, Ageing, Disease www.elixir-europe.org A European Infrastructure for Biological Information

2. ELIXIR Mission To construct and operate a sustainable infrastructure for biological information in Europe, to support life science research and its translation to medicine and the environment, the bio-industries and society. • Partners: 32 partners, 13 member states • Funding: 4.5 M€ from EU FP7 • Deliverable: Consortium agreement to define the scope of the infrastructure and how it will be constructed

3. Goals for ELIXIR • Optimal Data Management • Coordinated Data Resources with improved access • Integration and interoperability of diverse heterogeneous data • Good Value for Money • Forge Links to data in other related domains • A single European voice in international collaborations to influence global decisions and maintain open access to data • Enhance European competitiveness in bioscience industries • Address need for Increased Funding & its Coordination

4. Funders of Infrastructure National Government Funding Bodies; EMBL; EU Charities; Industry Data Resource Providers Core Resources Specialist (Many investigators - distributed) Data Providers Experimentalists Tool Providers Bioinformatics Groups Users Stakeholders

5. Europe USA Japan Why do we need ELIXIR? • Data Growth • Global context • Very large user community: • 3.3 m web hits/day • 20,000 unique users per day • Need to preserve data and make accessible to all • Impact on medicine & agriculture • Impact on society & bioindustries • Need for increased funding for biodata resources

6. Good Value for Money e.g. PDB Data collection In 2008 MEuro Annual Cost of PDB <1%

7. Two phases: Committee meetings of stakeholders to achieve consensus and make recommendations Jan 2008 – July 2009 NOW! Define scope and remit of ELIXIR Documentation and negotiation phase July 2009 – Dec 2010 Develop ‘International Consortium Agreement’ Define funding and legal model The Preparatory Phase project

8. Project management Data providers User communities Organisation and Legal Funding Physical infrastructure Data interoperability Literature Healthcare Chemistry, Plants, Agriculture & Environment Training Tools integration Feasibility studies Reporting and negotiation The Preparatory Phase project Elixir is organised into 14 work packages which have committees of (mainly) European experts associated with them.

9. ELIXIR Scientific and technical Structure

10. WP4: ELIXIR Legal and Governance ELIXIR Member States EMBL Scientific Advisory & Grant Committee ELIXIR Council ELIXIR Secretariat ELIXIR Executive Management (at EMBL-EBI) Heads of ELIXIR Nodes Committee ELIXIR Node 1 (EMBL-EBI) ELIXIR Node 2 ELIXIR Node 4 ELIXIR Node 3

11. ELIXIR Governance ELIXIR Member States ELIXIR EMBL Scientific Advisory & Grant Committee ELIXIR Council ELIXIR Secretariat ELIXIR Executive Management (at EMBL-EBI) Heads of ELIXIR Nodes Committee ELIXIR Node 1 (EMBL-EBI) ELIXIR Node 2 ELIXIR Node 4 ELIXIR Node 3

12. ELIXIR‘s tasks What will ELIXIR provide? Core and Specialist data resources Compute Centres Services for the user community

13. What are the responsibilities of the ELIXIR hub? Coordinate and support ELIXIR activities in Europe Quality control and organisation of selection process (peer review) for new nodes? Provide core data resources Host main data centre Ensure back up of core data resources Training and dissemination

14. ELIXIR Nodes – basic description • Prerequisites: • National or international legal entity or represented by legal entity • Capable of entering into contract with ELIXIR Hub • Provide additional funding sources (matching funds) • Capable of supporting one or more components of ELIXIR Infrastructure, e.g. of scientific or technical nature • ELIXIR components must have European service dimension • Other requirements to be determined (e.g. size, quality) • Selection and application process to be decided (e.g. calls for proposals)

15. What are the attributes of ELIXIR nodes? scientific excellence fit of thematic area reliability service-mentality coordinator of national activities? national contact point for ELIXIR availability of funding (50-100%) multi-year commitment (min. 5 years) supported by host country government subject to regular reviews participation in software and standards development

16. Resources needed for ELIXIR nodes Staff (incl. technical support staff) Buildings Equipment: computers Payment of subscriptions (eg for databases) and other fees for specialised services Participation in software development projects Participation in standards development activities

17. WP5 Activities: Funding • Engaging European research funders • Initial identification of funders’ aims and priorities – 2008 Survey • 3 meetings of WP5 Committee • Ongoing process of dialogue (& advocacy) • Working with Work Package 4 to develop ELIXIR model • Identify feasibility and acceptability for funders • UK Large Facilities Capital Fund support • Develop case for additional data storage facilities for EBI and supporting UK HTP sequencing activities

18. PRINCIPLES: Data sharing is the norm in the biomolecular domain - Public domain principles (can this be consistent with industry funding?) Data should be downloadable in their entirety Collaboration and avoidance of duplication in core data archives essential Data bases produced by research with primary responsibilities only to their research group are not Elixir Creative competition on services desirable Global context Standardisation WP2: Data Providers Recommendations

19. Literature and ontologies CitExplore, GO Databases: molecules to systems Genomes Ensembl, Ensembl Genomes, EGA Nucleotide sequence EMBL-Bank Proteomes UniProt, PRIDE Gene expression ArrayExpress Protein structure PDBe Protein families, motifs and domains InterPro Chemical entities ChEBI, ChEMBL Protein interactions IntAct Pathways Reactome Systems BioModels

20. 531 Databases surveyed 208 Responded, 323 did not Dead = no update since 2005

21. 200 Databases 700 People 100 Institutions 60 million web hits per month Total investment to date €308 million Annual cost €35 million BUT About 1/3 of responders report NO costs 60% of polled databases didn’t respond It is almost certain that the non-responders are smaller on average RECOMMENDATION Coordination and prioritisation, as well as stable funding, is needed for many of these resources Total European effort

22. Security of the databases (out of 208)

23. WP3: User Communities • User Survey: 800 responses • Long term support essential • Top 3 challenges: • Data integration; Format compatability; Website usability • Concerns • Data quality and measures; Quality of tools;Training • Need to consider different needs in different countries • Need for a plan for long-term maintenance of computational tools • Create mechanisms for long-term maintenance of bioinformatics tools • user-friendly & machine-friendly interfaces • Need for standards for formats and integration • Increased integration of databases, tools and between infrastructure domains • Need to provide mechanisms for prioritisation of need for resources

24. WP12 Tool integration priorities • Short term: • Access: Programatic access, (traditional clickable interfaces, downloads) • Basic infrastructure should work from the start in order to take off • Not new webservice technologies – winning ones largely identified* • Focus on accessibility, uptime, replication, testing and user scope • Well-maintained catalogs • Benchmarking frameworks (including maintenance) • Medium term: • User category-sensitive aspects • Recommended hardware for WSs • Advanced benchmarking and tool comparison • Tool termination policies • Long term: • End-user data and tool integration • Commercial tools adopt standards defined by public effort (long term goals hard to obtain from industry in particular big pharma)

25. Elixir Tool integration marketing bait ”Parsed on arrival”

26. WP8: Literature Europe will greatly benefit from a pan-European open access repository for scientific articles and related relevant text resources., interlinked with the other core data resources and embedded in text processing environments. ELIXIR should enable and maintain an infrastructure for the biomedical research community that: • brings together textual resources from different origins, 2) integrates the text resources into the biological databases, 3) allows efficient exploitation of the resources with automatic and interactive means and 4) supports formatting and semantics standards, to support scientific progress for the whole bio-med-chemical research community.

27. WP9: Healthcare Recommendations • Elixir should be a valuable resource for Healthcare • Contribute to translational, clinical research • Close collaboration with related infrastructures (e.g., biobanks, imaging, population-based registries/databases/trials) • Elixir must • Address the challenge of heterogeneous, often poorly structured data • develop and maintain nomenclatures and ontologies • support development of processing different data e.g. text & images) • include requirements from related domains (e.g., privacy protection) • facilitate communication with related domains (e.g., import and export of data, storing of meta data) • explicitly assign the responsibility to continuously and actively seek collaboration to certain partners or nodes to ensure accountability and transparency.

28. WP 10: Chemistry, Plants, Agriculture & Environment • Support / extend current core resources for • Nucleotide/protein sequence, genomes, structures, interactions etc. • Selected specialist resources migrated to Elixir infrastructure • Reduce complexity of informatics landscape, maintain functionality • Integration allows mining of combined data • Adopt key data standards and work for common infrastructure • Link to other ESFRI, non ESFRI European projects • Link to non European initiatives (NSF/iPlant, DOE/Camera)‏ • Free access to Elixir data and core analysis tools • Web based queries, programmatic access, download

29. WP11: Training Identified training issues in Europe: • Little or no coordination • Rapid evolution of bioinformatics resources • Lack of a centralised body for guidance; • Lack of recognition of the importance of bioinformatics user training, even within the bioinformatics community. Elixir recommendations:Link the development of data resources to the provision of training materials;Create a training support unit that will: a) provide a centralised training registry; b) provide support for trainers throughout Europe c) develop benchmarking and evaluation systems; d) provide mechanisms for developing new training programmes e) act as a single point of contact for national and pan-European training

30. ESFRI Biology Research Infrastructure proposals. Hit BBMRI INSTRUCT Infrafrontier ECRIN EATRIS (Mouse) (Structural biology) (Biobanking) (Translational Research) (Clinical Trials) Research Discovery Development Lead Opt Preclinical Phase I Phase II Target ID Target Val Lead Phase III ELIXIR (Biological Information) 30

31. Many meetings!! Versailles 9 December 2008 ECRI 2008. European Conference on Research Infrastructure Nancy 21 November 2008 L’Institut de l’Information Scientifique et Technique Launch of Standards-based Infrastructure with Distributed Resources (SIDR) Paris 21st & 22nd October e-IRG open workshop organized by GIP RENATER under the French EU-presidency Information exchange between the ESFRI PPPs & the e-Infrastructure Community Bergen October 9-10 1) Norwegian Bioinformatics Forum 2) Meeting with Stakeholders & Research Council Make case for Norwegian Involvement in ELIXIR Innsbruck, 1-4 Oct 2008 3rd ESF Functional Genomics & Disease Conference Presentation at BIOSAPIENS symposium 11th-12th September 2008, Duesseldorf, Germany ERASysBio 2nd Meeting of European Systems Biology Centres Presentation on ELIXIR SB Feasibility Study Edinburgh 8-11th September e-Science All hands Meeting Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructures Munich 20th August PARADE partners planning meeting Presentation on EBI contribution to PARADE Helsinki 11 August Finnish Stakeholders Meeting Make case for Finnish involvement in ELIXIR 9th of July in Lisbon First meeting of national network of bioinformatics Presentation and meet with government representatives July 4th in Rome. Meeting of the BITS (Bioinformatics Italian Society) Perspectives of Bioinformatics in Europe (e.g. Elixir project, etc.). Brussels on Wednesday 11th June ESFRI BMS coordinator meeting Munich Airport Marriott Hotel June 02 to June 03. Infrafrontier Kickoff European Parliament Wednesday, May 28th, 2008 Invitation from BBMRI on behalf of Paul Rübig, MEP Seminar on plans for a pan-European biobanking and biomolecular resources RI. INSTRUCT Kick-Off meeting Paris on May 6th 2008 The Hague Wednesday 12 March Netherlands Stakeholders and Key Opinion Leaders meeting 11-14 March 2008 in Amsterdam. Life Watch Kick-off Meeting Brdo, Slovenia 5 - 6 March 2008 Slovenian Presidency Conference Research Infrastructures and their Structuring Dimension within the ERA

32. Prep. Phase Interim Phase Permanent Phase ELIXIR Dec 2010 Dec 2016 EMBL Indicative Scheme Dec 2011 Dec 2016 Dec 2021 EU Framework Programme 7 EU FP8 Dec 2013 Dec 2020 ELIXIR evolution Nov 2007

33. Next Steps • On course to produce reports from all surveys and WPs by mid July • Many visits to member countries are ‘in progress’ – to identify unique contributions and requirements • Further discussions needed with international colleagues • THEN – discussions on International Consortium Agreement and Funding

34. Benefits of ELIXIR This infrastructure will contribute to European science by: • Optimising access and exploitation of life-science data. • Ensuring longevity of the data and protecting investments already made in research which collected the data, • Increasing the competence and size of the already-large user community by strengthening national efforts in training and outreach. • Enhance the global success and influence of Europe in life-science research and industry.