Developments in Metabolomics leading to PhenoMeNal

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Christoph Steinbeck

Talk presented at the de.NBI (German Network for Bioinformatics) symposium 2017 in Bielefeld, Germany

Science

Christoph Steinbeck
and the
PhenoMeNal consortium
European Bioinformatics Institute, Hinxton
Friedrich-Schiller-University, Jena
Large scale computing with medical
metabolic phenotyping data

The
European Bioinformatics Institute
(EBI)

Friedrich-Schiller-University Jena, Germany
Founded 1558

Metabolomics On The Rise
Source: Google Scholar

Metabolomics On The Rise
ELIXIR
PRIDE
MetaboLights
PhenoMeNal
MSI
COSMOS
Metabolomics
Workbench
Source: Google Scholar

Phenome Centres
• London
• Birmingham
• Shanghai
• NIH RCMRCs
• …

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

Make data FAIR
-
Share them
-
Free and Open

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.

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

Claire O’Donovan
Head of Metabolomics Services
European Bioinformatics Institute

Sansone,… Steinbeck et al. (2012)
Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
Data Submission to MetaboLights

Sansone,… Steinbeck et al. (2012)
Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
ControlledVocabularies
Ontologies
Data Submission to MetaboLights

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

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

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

Global Standards
and
Data Exchange
in
Metabolomics

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

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

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

An e-infrastructure for
Large Scale Computing
with Medical
Metabolomics Data

Large Scale Computing
with Medical
Metabolomics Data

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Statistical analysis
By E. Thevenot, P. Roger Mele

The European Open Science Cloud
As part of EOSC and
GO FAIR,
PhenoMeNal helps
building a hub for
verifying
FAIR metabolomics
data

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

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Developments in Metabolomics leading to PhenoMeNal

1. Christoph Steinbeck and the PhenoMeNal consortium European Bioinformatics Institute, Hinxton Friedrich-Schiller-University, Jena Large scale computing with medical metabolic phenotyping data

2. The European Bioinformatics Institute (EBI)

3. The European Bioinformatics Institute (EBI)

4. The European Bioinformatics Institute (EBI)

5. The European Bioinformatics Institute (EBI)

6. Friedrich-Schiller-University Jena, Germany Founded 1558

7. Metabolomics On The Rise Source: Google Scholar

8. Metabolomics On The Rise ELIXIR PRIDE MetaboLights PhenoMeNal MSI COSMOS Metabolomics Workbench Source: Google Scholar

9. Phenome Centres • London • Birmingham • Shanghai • NIH RCMRCs • …

10.

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

12. How do you make sense of all that data?

13. Make data FAIR - Share them - Free and Open

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. Claire O’Donovan Head of Metabolomics Services European Bioinformatics Institute

17. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. Data Submission to MetaboLights

18. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Data Submission to MetaboLights

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

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 Standards and Data Exchange in Metabolomics

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.

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

27.

28.

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

30. An e-infrastructure for Large Scale Computing with Medical Metabolomics Data

31. Large Scale Computing with Medical Metabolomics Data

32. Large Scale Computing with Medical Metabolomics Data

33. Generic Cloudiﬁcation

34.

35. Continuous Integration via Jenkins

36. More on technology and micro-services in Ola Spjuth’s talk