PhenoMeNal presentation given at STFC-ELIXIR Meeting Hinxon

1. Large scale computing with
medical metabolic
phenotyping data
Christoph Steinbeck and the
PhenoMeNal consortium
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. Metabolites:
Small molecules in biological organisms

8. No biopolymers
• No DNA
• No Proteins
• No Sugar Polymers

9. Metabolomics
Measures occurrence and
concentrations of many small
molecules (metabolites) in an
organism at once.

10. Organism Parts

11. Nuclear Magnetic Resonance
(NMR)
Mass Spec
Metabolomics uses a wide-range of
analytical techniques

12. source: http://www.csfmetabolome.ca

13. source: http://www.csfmetabolome.ca

14. source: http://www.csfmetabolome.ca

15. Untargeted Metabolomics
of Cerebrospinal Fluid
AD – red; MCI- blue
Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN)
AD – red; CN- blue

16. Untargeted Metabolomics
of Cerebrospinal Fluid
AD – red; MCI- blue
Alzheimer’s Disease (AD), Mild Cognitive Impairment (MCI), Cognitive Normal (CN)
AD – red; CN- blue
Basis for a
diagnostic tool

17. 0597

18. 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.

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

20. Data growth in EBI data repositories

21. Data growth in EBI data repositories
3-month
doubling time
for
Metabolomics

22. 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

23. Global Collaboration in
Metabolomics and the
BioSciences

24. 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

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

26. What’s next?

27. Metabolomics can contribute
to a better medicine
predictive
preventive
personalizedparticipatory

28. •500 Million people in European Union
•Full Genomes (soon for less than $1000 p. P.)
•Urine/Blood Metabolome < 20 Euros per Patient

29. Metabolomics is taking off world-wide

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

32. > 100,000 patient samples / year
> Several PetaBytes/year
=> ExaBytes of human data at
moderate scale-up

33. Large Scale Computing
with Medical
Metabolomics Data
• EBI lead
• H2020
• 3Years
• 13 Partners
• 8 Mio €
• 830 PM
• Kick-off 9/15
• H2020 e-infra

34. Large Scale Computing
with Medical
Metabolomics Data

36. Large Scale Computing
with Medical
Metabolomics Data

37. PhenoMeNal
Cooperative Ecosystem
EGI
ELIXIR cloud activities
BioMedBridges
CORBEL
BBMRIPhenoMeNal
iSphere
IndigoDataCloud
Phenomics User Community
GCE EC2 OpenStack
i~HD

38. Funding and Collaborators
UK Research Councils (BBSRC, MRC)
European Commission

39. Thanks for your attention

40. Metabolights-help@ebi.ac.uk
Thank you!