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Sharing data from clinical and medical research

Talk by Christoph Steinbeck, European Bioinformatics Institute (EMBL-EBI) on challenges for data sharing of clinical data in metabolomics research. This workshop was co-organised with the European BBMRI Biobanking infrastructure as part of the BioMedBridge symposium at the Wellcome Trust Conference Centre in Hinxton, UK.

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Sharing data from clinical and medical research

  1. 1. Sharing data from clinical and medical research Christoph Steinbeck European Bioinformatics Institute (EMBL-EBI)
  2. 2. Post Genomic Era Christoph Steinbeck European Bioinformatics Institute (EMBL-EBI) [O]ur understanding of the human genome has changed in the most fundamental ways.The small number of genes -- some 30,000 -- supports the notion that we are not hard wired.We now know the notion that one gene leads to one protein, and perhaps one disease, is false. CraigVenter, June 2001
  3. 3. Genes are not the full story
  4. 4. Nutrition Exercise Disease Age Drugs Environment Phenome/ Exposome
  5. 5. The Metabolome is the most accessible and dynamically changing Molecular Phenotype
  6. 6. Investigating Metabolomes at Large Scale to disentangle the exposome conundrum
  7. 7. Phenome Centres popping up all over the world • London • Birmingham • Shanghai • United States NIH RCMRCs • …
  8. 8. Time Scales: Patient Journey vs Population Modelling
  9. 9. > 100,000 patient samples / year > Several PetaBytes/year => ExaBytes of human data at moderate scale-up
  10. 10. Open BioData Sharing • • Commercial community efforts (23AndMe …) • Quantified-Self revolution • Individual efforts • Apple health kit • Who will write the FaceBook for Personal Medical Data?
  11. 11. 23AndPee
  12. 12. MetaboLights open-access, cross-species, cross-application, long-term supported Salek, R.M., Haug, K. and Steinbeck, C. (2013) Dissemination of metabolomics results: role of MetaboLights and COSMOS. Gigascience, 2:8.
  13. 13. MetaboLights Database Experimental Repository Reference Layer Chemistry Spectroscopy Biology AnalysisTools Primary Literature Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
  14. 14. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Minimum Information Standards
  15. 15. Data growth in EBI data repositories 3-month doubling time for Metabolomics MetaboLights is now the recommended repository for the Nature journals, EMBO journal, PLOS journals, Metabolomics Journal and others
  16. 16. Global Collaboration in Metabolomics and the BioSciences
  17. 17. COSMOS COrdination of Standards in MetabolOmicS European FP7 coordination action coordinated by us at EMBL-EBI, Hinxton, Cambridge • Create missing standards & formats • Define workflows for dissemination • Create world-wide data network
  18. 18. MetabolomeXchange 2014 • Global network for exchange and discoverability of metabolomics data • Includes study as well as reference data
  19. 19. - Coordination of Standards in Metabolomics
  20. 20. What’s next?
  21. 21. From Molecules to Medicine
  22. 22. Large scale computing with medical metabolic phenotyping data Christoph Steinbeck and the PhenoMeNal consortium European Bioinformatics Institute (EMBL-EBI)
  23. 23. PhenoMeNal: Building an e-Infrastructure for Large Scale Computing with Medical Metabolic Phenotyping Data • EBI lead • H2020 • 3Years • 13 Partners • 8 Mio € • 830 PM • Kick-off 9/15
  24. 24. PhenoMeNal: Large Scale Computing with Medical Metabolic Phenotyping Data
  25. 25. PhenoMeNal: Large Scale Computing with Medical Metabolic Phenotyping Data
  26. 26. Data Sharing Issues in Clinical Metabolomics
  27. 27. Data Sharing Issues in Metabolomics
  28. 28. Data Sharing Issues in Metabolomics
  29. 29. Data Sharing Issues in Metabolomics
  30. 30. Thanks for your attention