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.

1. Sharing data from
clinical and medical
research
Christoph Steinbeck
European Bioinformatics Institute
(EMBL-EBI)

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. Genes are not the full story

5. Nutrition
Exercise
Disease
Age
Drugs
Environment
Phenome/
Exposome

6. The Metabolome
is the most accessible and
dynamically changing
Molecular Phenotype

7. Investigating Metabolomes
at Large Scale
to disentangle the exposome conundrum

8. Phenome Centres popping
up all over the world
• London
• Birmingham
• Shanghai
• United States NIH RCMRCs
• …

10. Time Scales:
Patient Journey vs Population Modelling

11. > 100,000 patient samples / year
> Several PetaBytes/year
=> ExaBytes of human data at
moderate scale-up

12. Open BioData Sharing
• OpenGenomes.org
• Commercial community efforts (23AndMe …)
• Quantified-Self revolution
• Individual efforts
• Apple health kit
• Who will write the FaceBook for Personal
Medical Data?

13. 23AndPee

14. MetaboLights
http://www.ebi.ac.uk/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.

15. MetaboLights Database
Experimental Repository
Reference Layer
Chemistry Spectroscopy Biology
AnalysisTools
Primary Literature
Primary data and Meta-Data, Spectra, Protocols, Synopses, ...

16. Sansone,… Steinbeck et al. (2012)
Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
ControlledVocabularies
Ontologies
Minimum Information Standards

17. 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

18. Global Collaboration in
Metabolomics and the
BioSciences

19. 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

20. MetabolomeXchange 2014
• Global network for exchange and
discoverability of metabolomics data
• Includes study as well as reference data

21. - Coordination of Standards in Metabolomics

22. What’s next?

23. From Molecules to Medicine

24. Large scale computing with
medical metabolic
phenotyping data
Christoph Steinbeck and the
PhenoMeNal consortium
European Bioinformatics Institute
(EMBL-EBI)

25. 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

26. PhenoMeNal: Large Scale Computing
with Medical Metabolic Phenotyping Data

27. PhenoMeNal: Large Scale Computing
with Medical Metabolic Phenotyping Data

28. Data Sharing
Issues
in Clinical
Metabolomics

29. Data Sharing Issues
in Metabolomics

30. Data Sharing
Issues
in Metabolomics

31. Data Sharing
Issues
in Metabolomics

32. Thanks for your attention