Developing an Efficient Infrastruture, Standards and Data-Flow for Metabolomics

Developing an Efficient Infrastructure, Standards and Data-Flow for Metabolomics

Christoph Steinbeck

European Bioinformatics Institute(EMBL-EBI)

The European Bioinformatics Institute

(EBI)

The European Bioinformatics Institute

(EBI)

The European Bioinformatics Institute

(EBI)

The European Bioinformatics Institute

(EBI)

The European Molecular Biology Laboratory

(EMBL)

A basic research institute funded by public research monies from 20 member states.

European Bioinformatics Institute (EBI)

European Bioinformatics Institute (EBI)Genes, genomes & variation

Literature & ontologies Europe PubMed Central Gene Ontology Experimental Factor Ontology Molecular structures

Protein Data Bank in Europe Electron Microscopy Data Bank

European Nucleotide Archive 1000 Genomes

Gene, protein & metabolite expression

Protein sequences, families & motifs

Chemical biology

Reactions, interactions & pathways Systems

Ensembl Ensembl Genomes

European Genome-phenome Archive Metagenomics portal

European Bioinformatics Institute (EBI)Genes, genomes & variation

Literature & ontologies Europe PubMed Central Gene Ontology Experimental Factor Ontology Molecular structures

Protein Data Bank in Europe Electron Microscopy Data Bank

European Nucleotide Archive 1000 Genomes

Gene, protein & metabolite expression

Protein sequences, families & motifs

Chemical biology

Reactions, interactions & pathways Systems

Ensembl Ensembl Genomes

European Genome-phenome Archive Metagenomics portal

European Bioinformatics Institute (EBI)Genes, genomes & variation

Literature & ontologies Europe PubMed Central Gene Ontology Experimental Factor Ontology Molecular structures

Protein Data Bank in Europe Electron Microscopy Data Bank

European Nucleotide Archive 1000 Genomes

Gene, protein & metabolite expression

Protein sequences, families & motifs

Chemical biology

Reactions, interactions & pathways Systems

Ensembl Ensembl Genomes

European Genome-phenome Archive Metagenomics portal

Nutrition

Exercise

Disease

AgeDrugs

Environment

Phenome/Exposome

The Metabolome is the most accessible and

dynamically changing Molecular Phenotype

Organism Parts

Nuclear Magnetic Resonance (NMR)

Mass Spec

Metabolomics uses a wide-range of analytical techniques

What do the EBI databases do? Labs around the world send us their data and

we…

Archive it

Classify itShare it with other data providers

Analyse it

…provide tools to help researchers

use it

A collaborative enterprise

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

Ana

lysi

s To

ols

Primary Literature

Primary data and Meta-Data, Spectra, Protocols, Synopses, ...

www.ebi.ac.uk/metabolights (metabolights.org, metabolights.eu)

Data growth in EBI data repositories

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

repositoryfor the Nature journals,

EMBO journal, PLOS journals, Metabolomics

Journal and others

MetaboLights Stats May 2016

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

The MetaboLights Reference Layer

•8.7 mio eukaryotic species on earth (+- 1.3mio)

•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified

•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced

•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced

•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced

What about completed metabolomes?

•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced

What about completed metabolomes?

Species Metabolomes are being assembled on the fly

right now through data sharing in Metabolomics

Repository Entry

Repository Entry

Reference Layer

7 most annotated metabolomes in MetaboLights

Current and Future Work

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

Phenome Centres founded all over the world

• London

• Birmingham

• Shanghai

• NIH RCMRCs

• …

> 100,000 patient samples / year> Several PetaBytes/year

=> ExaBytes of human data at moderate scale-up

Large Scale Computing with Medical Metabolomics Data

• EBI lead• H2020• 3 Years• 13 Partners• 8 Mio €• 830 PM• Kick-off 9/15• H2020 e-infra

Large Scale Computing with Medical Metabolomics Data

Large Scale Computing with Medical Metabolomics Data

Large Scale Computing with Medical Metabolomics Data

Large Scale Computing with Medical Metabolomics Data

Networking Activities - Ecosystem

ELIXIR cloud activities

BioMedBridges

CO

RBEL

BBMRIPhenoMeNal

Euro

pean

Ope

n Sc

ienc

e cl

oud

Indi

go D

ata

Clo

ud Phenomics User Community

EGI GCE EC2 OpenStack

i~H

D

Industry-grade orchestration

Networking Activities -EOSC

AspartofEOSCandGOFAIR,PhenoMeNalispositioningitselfashubforverifyingFAIRmetabolomicsdata

The Next 5 Years

• Standardised dissemination and analysis of big data in Metabolomics

• Cloud-based workflows for Phenomics

• Assembly of model species metabolomes

• Literature-mining

• Comprehensive structure elucidation of unknown metabolites

The Next 5 Years for MetaboLights

• Maintenance and improvement

• Advanced metadata-based data analysis and visualisation

• Slice and Dice

• Improved reference layer

• Web services access

• MetaboLights Cloudified Version

• Online creation of MetaboLights ISA-Tab studies

• Standardisation, Training and Outreach

Funding and CollaboratorsUK Research Councils (BBSRC, MRC) European Commission

Slides on http://www.slideshare.net/csteinbeck

Metabolights-help@ebi.ac.uk

Thank you!