1. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org EGI 2015, Lisbon, 18 May 2015 Rafael C Jimenez, ELIXIR CTO ELIXIR EXCELERATE Use Cases

2. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org ELIXIR

3. European distributed Research Infrastructure for biological research 3 Provide data services essential to enable, sustain, or enhance biological science

4. ELIXIR Members 4 Connects national centers and EMBL-EBI Participated by major bioinformatics service providers (~130) and supported by 17 EU member states 12 Members Czech Republic, Estonia, EMBL- EBI, Denmark, Finland, Israel, Netherlands, Norway, Portugal, Switzerland, Sweden, UK 6 Observers Belgium, Greece, France, Italy, Slovenia, Spain

5. Strategic drivers 1.Establish a distributed infrastructure to scale with the challenge of data growth 2.Secure and deliver the core data resources underpinning life science research 3.Provide discoverable tools, services and connectors to drive data access and exploitation 4.Provide robust technical platforms and clouds for secure data access, data exchange and compute 5.Develop and maintain standards for data management, reuse and integration 6.Drive partnerships with user communities and other organisations to ensure high impact 7.Close the computational biology skills gap through a comprehensive training programme for professionals 8.Support innovation in big data biology

6. Infrastructure for Life Sciences 6 Services & connectors to drive access and exploitation Integration and interoperability of data and services Sustain core data resources Access, Exchange & Compute on sensitive data Compute Dat a Standards Tools Training Professional skills for managing and exploiting data Access, Search, Analysis … Integration, Optimization, Privacy, … Storage, Network & Computing Formats, Ontologies, Guidelines, … Scientific & technical http://www.elixir-europe.org/sites/default/files/documents/elixir_scientific_programme_final.pdf ELIXIR programme

7. Technical activities Node Pilots Projects EXCELERATE, CORBEL, BioMedBridges, EGI ELIXIR Competence Center, Tryggve, EUDAT2, NIH-ELIXIR identifiers, …

8. Plant Marine Rare disease Human research data Data management plans … Service Registry Benchmarking Workflows …. Standards Identity management FAIR … Data transfer Cloud services AAI … Training portal Train the trainer E-learning … Metrics & Monitoring Data life cycle Data curation... ELIXIR-EX WP4 CORBEL WP6 EGI-CC Pilots & CoS … ELIXIR-EX WP4 CORBEL WP6 Pilots & CoS … ELIXIR-EX WP4 ELIXIR-EX WP2 Pilots & CoS … ELIXIR-EX WP4 Sustainability WG Pilots & CoS … ELIXIR-EX WP4 CORBEL WP9 GOBLET RI-Train Pilots & CoS … DataToolsInteroperabilityComputeTraining Platform activities Node activities

9. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org EXCELERATE

10. Infradev3 proposal H2020 – Submitted in January – Expected to start in autumn (if awarded) Goal – Accelerate implementation of ELIXIR Implementation of the ELIXIR Scientific Programme Engagement with user communities Integration of national ELIXIR Nodes Coordination of a distributed infrastructure

11. EXCELERATE

12. Marine metagenomic infrastructure as driver for research and industrial innovation

13. Objectives/Tasks Development of standards for the marine domain – Data format conventions – Reporting guidelines – Validation tools Establishment of marine specific data resources Development of tools and pipelines for metagenomics analysis Development of a search engine for interrogation of marine metagenomics datasets Training workshops for end users Marine metagenomics

14. Data producer ENAUniProt Marine metagenomics Submission Import MGP Marine metagenomics MetaPipe Replication Bioinformatician Analysis Scientist Analysis EMBL-EBIELIXIR NO Marine metagenomics Release metadata Content + Structure Access

16. Integrating Genomic and Phenotypic Data for Crop and Forest Plants

17. Challenges Phenotypic data is a major challenge Very diverse Represented in non-standard ways No central repository (nor is there likely to be one) for all data

18. Objectives/Tasks Make data interoperable – Development of controlled vocabularies – Adoption of standardized common APIs Annotate and submit key exemplar datasets to relevant public archives. Engage industry in defining priorities and present them showcases. Delivering specific training for the use of developed resources. Plants Genomic and Phenotypic Data

19. pkersey@ebi.ac.uk10.06.201619 ELIXIR service registry Search Engine Implementing shard Search API Underlying DB Retrieval API Possibly hosted by ELIXIR Hosted remotely by nodes or other participants User farmELIXIR farmCommercial farm Node farm Retrieval engine Plants Genomic and Phenotypic Data Paul Kersey

20. Infrastructure for Rare Disease research

21. Objectives/Tasks Build portfolio of data resources and analysis tools – Continuous monitoring of resources and tools in Rare- diseases – Creation of reference datasets adequate for the specific assessment of methods and standards in the area of rare- diseases – Annotation in the ELIXIR registry. Implementation of a technical framework for the comparison and standardization of services Training workshops targeting user communities Rare diseases

22. Scientist Clinician Doctor ELIXIR Rare Disease Portal API Search … Biobank catalogue API … Patient catalogue API Rare diseases EGA API Genomics studies Data producer AAI

24. 24 Example Task 8.2: Linked data; across resource questions ELIXIR login Patient Catalogue R1 R2 Rn Phenotype Servers Biobank Catalogue B1 B2 Bn Variant Priorization EGA Genomics Repository Data Processing Which biobanks have biosamples from patients with a disease onset between age X-Y (registry/clinical data) and diagnosed with mutation Z (omics data)?

25. Framework for secure archiving, dissemination and analysis of human access-controlled data; enabling biobanks, cohorts and local resource services to leverage the EGA

26. Objectives/Tasks Secure data and metadata submission tools – Large scale submissions – Portable submission toolkit Integrating centralized and distributed projects – EGA programmatic interfaces and ELIXIR endorsed formats – Access management workflow support – Support distributed local hosting of datasets Federated authentication, large scale data management, and secure clouds in practice – Large scale data mirroring support – EGA data access authorization integration. – Data access APIs Human access-controlled data

27. Secure Compute Clouds High speed encrypted data transfer GridFTP/Globus/Aspera Secure data access remote API ( GA4GH ) Sequencing centers Data Users Data Archiving Bringing users to data Data Generation Managing Access Data Owner Data Access Agreement Data Access Committee Data Request Authorization Management Tools ( EGA and CSC REMS ) Federated Authentication Authorization Dataset registry Data transfer hub Policy and Legal Framework Services and Coordination Local EGA Bringing data to users Supporting sample logistics Human access-controlled data

28. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org Thank you! Questions?