multi-omics bioinformatics across application domains
TRANSCRIPT
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Multi-Omics Bioinformatics across Application Domains
Christoph Steinbeck
European Bioinformatics Institute(EMBL-EBI)
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The European Molecular Biology Laboratory
Structural biology
Grenoble, France
Bioinformatics
Hinxton, Cambridge, UK
Structural biology
Hamburg, Germany
Main laboratory
Heidelberg, Gemany
Monterotondo, Rome, Italy
Neuroscience
• 60 nationalities• 1800 personnel
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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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A word about BrExit: EMBL member states
Austria, Belgium, Croatia, Czech Republic, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the UK
Associate member states: Argentina, Australia
Prospect member states: Hungary, Poland, Slovak Republic
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Our funders
• EMBL-EBI is primarily funded by EMBL member states.
• Other major funders:• European Commission• Research Councils UK• National Institutes
of Health• Wellcome Trust• Industry Programme
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Data and tools to support life-science research
www.ebi.ac.uk/services
Bioinformatics services
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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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Big data, big demand
~18.5 million requests to EMBL-EBI
websites every day
60 petabytesof EMBL-EBI storage capacity
EMBL-EBI handles
9.2 million jobs on average per month
Scientists at over
5 million unique sites use
EMBL-EBI websites
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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.
Craig Venter, June 2001
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Genes are not the full story
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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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Metabolomics
Measures occurrence and concentrations of many small molecules (metabolites) in an organism at once.
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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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Metabolomics has taken off world-wide
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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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Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.
Metabolites. 2016 Feb 15;6(1)
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Species Metabolomes are being assembled on the fly
right now through data sharing in Metabolomics
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Experimental Repository
Reference Layer
Chemistry Spectroscopy Biology
Ana
lysi
s To
ols
Primary Literature
Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
MetaboLights Database at the EBI
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MetaboLights Database at the EBILabs 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 Database at the EBILabs 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
Data at the EBI can be
used freelyby anyone for any
purpose
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MetaboLights Repository at the EBILabs 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
EBI databases are supported over
decades
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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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Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
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Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
Controlled VocabulariesOntologies
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Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data.
Nature Genetics, 44, 121–126.
Controlled VocabulariesOntologies
Minimum Information Standards
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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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30 most annotated metabolomes in MetaboLights
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1600 metabolome sizes in MetaboLights on a log scale
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Number of Studies in MetaboLights per Species
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Shareprivateprepublicationstudieswithreviewersandothertrustedparties.
BiocratesXMLwithrawdataisannotatedanduploaded
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Multi-Omics Data Handling
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A Case for Deep Metabolome Annotation
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A Case for Deep Metabolome AnnotationHelp building species metabolomes
•Submit your metabolomics study to MetaboLights•Submit data publications (e.g. to NATURE Scientific Data)
•Be highly cited :)
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Slides athttps://www.slideshare.net/csteinbeck
Funding
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Thanks for your attention
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