Multi-Omics Bioinformatics across Application Domains
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Talk held at the 39th International Conference on Environmental & Food Monitoring (ISEAC) in Hamburg on 20 July 2016
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Multi-Omics Bioinformatics across Application Domains
- 1. Multi-Omics Bioinformatics across Application Domains Christoph Steinbeck European Bioinformatics Institute (EMBL-EBI)
- 2. 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
- 7. 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
- 8. 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
- 9. Data and tools to support life-science research www.ebi.ac.uk/services Bioinformatics services
- 10. 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
- 11. Big data, big demand ~18.5 million requests to EMBL-EBI websites every day 60 petabytes of 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
- 12. 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
- 13. Genes are not the full story
- 17. The Metabolome is the most accessible and dynamically changing Molecular Phenotype
- 18. Metabolomics Measures occurrence and concentrations of many small molecules (metabolites) in an organism at once.
- 19. Organism Parts
- 20. Nuclear Magnetic Resonance (NMR) Mass Spec Metabolomics uses a wide-range of analytical techniques
- 21. Metabolomics has taken off world-wide
- 24. •8.7 mio eukaryotic species on earth (+- 1.3mio)
- 25. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified
- 26. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 27. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 28. •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?
- 29. •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?
- 30. 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)
- 31. Species Metabolomes are being assembled on the fly right now through data sharing in Metabolomics
- 32. Experimental Repository Reference Layer Chemistry Spectroscopy Biology AnalysisTools Primary Literature Primary data and Meta-Data, Spectra, Protocols, Synopses, ... MetaboLights Database at the EBI
- 33. MetaboLights Database at the EBI Labs around the world send us their data and we… Archive it Classify it Share it with other data providers Analyse it …provide tools to help researchers use it A collaborative enterprise
- 34. MetaboLights Database at the EBI Labs around the world send us their data and we… Archive it Classify it Share it with other data providers Analyse it …provide tools to help researchers use it A collaborative enterprise Data at the EBI can be used freely by anyone for any purpose
- 35. MetaboLights Repository at the EBI Labs around the world send us their data and we… Archive it Classify it Share it with other data providers Analyse it …provide tools to help researchers use it A collaborative enterprise EBI databases are supported over decades
- 36. Data growth in EBI data repositories
- 37. Data growth in EBI data repositories 3-month doubling time for Metabolomics
- 38. 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
- 39. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126.
- 40. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies
- 41. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Minimum Information Standards
- 42. Repository Entry
- 43. Repository Entry
- 44. Reference Layer
- 48. 7 most annotated metabolomes in MetaboLights
- 49. 30 most annotated metabolomes in MetaboLights
- 50. 1600 metabolome sizes in MetaboLights on a log scale
- 51. Number of Studies in MetaboLights per Species
- 57. A Case for Deep Metabolome Annotation
- 58. A Case for Deep Metabolome Annotation Help building species metabolomes •Submit your metabolomics study to MetaboLights •Submit data publications (e.g. to NATURE Scientific Data) •Be highly cited :)
- 60. Thanks for your attention