Developing an Efficient Infrastruture, Standards and Data-Flow for Metabolomics
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Transcript of Developing an Efficient Infrastruture, Standards and Data-Flow for Metabolomics
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Developing an Efficient Infrastructure, Standards and Data-Flow for Metabolomics
Christoph Steinbeck
European Bioinformatics Institute(EMBL-EBI)
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The European Bioinformatics Institute
(EBI)
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The European Bioinformatics Institute
(EBI)
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The European Bioinformatics Institute
(EBI)
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The European Bioinformatics Institute
(EBI)
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The European Molecular Biology Laboratory
(EMBL)
A basic research institute funded by public research monies from 20 member states.
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European Bioinformatics Institute (EBI)
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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
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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
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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
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Nutrition
Exercise
Disease
AgeDrugs
Environment
Phenome/Exposome
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The Metabolome is the most accessible and
dynamically changing Molecular Phenotype
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Organism Parts
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Nuclear Magnetic Resonance (NMR)
Mass Spec
Metabolomics uses a wide-range of analytical techniques
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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
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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.
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MetaboLights Database
Experimental Repository
Reference Layer
Chemistry Spectroscopy Biology
Ana
lysi
s To
ols
Primary Literature
Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
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www.ebi.ac.uk/metabolights (metabolights.org, metabolights.eu)
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Data growth in EBI data repositories
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Data growth in EBI data repositories
3-month doubling time
for Metabolomics
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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
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MetaboLights Stats May 2016
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Global Standards and
Data Exchange in
Metabolomics
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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
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MetabolomeXchange 2014
• Global network for exchange and discoverability of metabolomics data
• Includes study as well as reference data
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The MetaboLights Reference Layer
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•8.7 mio eukaryotic species on earth (+- 1.3mio)
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•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified
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•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced
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•8.7 mio eukaryotic species on earth (+- 1.3mio)•1.2 mio species identified and classified•3000 - 4000 complete species genomes sequenced
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•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?
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•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?
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Species Metabolomes are being assembled on the fly
right now through data sharing in Metabolomics
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Repository Entry
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Repository Entry
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Reference Layer
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7 most annotated metabolomes in MetaboLights
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Current and Future Work
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•500 Million people in European Union•Full Genomes (soon for less than $1000 p. P.)•Urine/Blood Metabolome < 20 Euros per Patient
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Phenome Centres founded all over the world
• London
• Birmingham
• Shanghai
• NIH RCMRCs
• …
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> 100,000 patient samples / year> Several PetaBytes/year
=> ExaBytes of human data at moderate scale-up
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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
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Large Scale Computing with Medical Metabolomics Data
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Large Scale Computing with Medical Metabolomics Data
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Large Scale Computing with Medical Metabolomics Data
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Large Scale Computing with Medical Metabolomics Data
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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
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Networking Activities -EOSC
AspartofEOSCandGOFAIR,PhenoMeNalispositioningitselfashubforverifyingFAIRmetabolomicsdata
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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
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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
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Funding and CollaboratorsUK Research Councils (BBSRC, MRC) European Commission
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Slides on http://www.slideshare.net/csteinbeck