Building a Model Organism Metabolome Database
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Talk given at the symposium about government-funded databases and open chemistry at the national meeting of the American Chemical Society in Washington, 21 Aug 2017
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Building a Model Organism Metabolome Database
- 1. Building a Model Organism Metabolome Database Christoph Steinbeck European Bioinformatics Institute, Cambridge, UK Friedrich-Schiller-University, Jena, Germany
- 7. 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
- 9. •8.7 mio eukaryotic species on earth (+- 1.3mio)
- 10. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified
- 11. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 12. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 13. •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?
- 14. •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?
- 15. 1 10 100 1000 10000 100000 1000000 10000000 100000000 Metabolites in Human Metabolites in Microbes Compounds in ChEBI V154 Metabolites in HMDB V3.6 Metabolites in Plants Compounds in ChEMBL V23 Compounds in PubChem V8-2017 Species Metabolomes and How Little We Know (2008 vs 2016)
- 16. 1 10 100 1000 10000 100000 1000000 10000000 100000000 Metabolites in Human Metabolites in Microbes Compounds in ChEBI V154 Metabolites in HMDB V3.6 Metabolites in Plants Compounds in ChEMBL V23 Compounds in PubChem V8-2017 Species Metabolomes and How Little We Know (2008 vs 2016) 80,000
- 17. 1 10 100 1000 10000 100000 1000000 10000000 100000000 Metabolites in Human Metabolites in Microbes Compounds in ChEBI V154 Metabolites in HMDB V3.6 Metabolites in Plants Compounds in ChEMBL V23 Compounds in PubChem V8-2017 Species Metabolomes and How Little We Know (2008 vs 2016) 80,000 200,000
- 18. 1 10 100 1000 10000 100000 1000000 10000000 100000000 Metabolites in Human Metabolites in Microbes Compounds in ChEBI V154 Metabolites in HMDB V3.6 Metabolites in Plants Compounds in ChEMBL V23 Compounds in PubChem V8-2017 Species Metabolomes and How Little We Know (2008 vs 2016) 80,000 200,000 2,000,000
- 19. Metabolomics has taken off world-wide
- 20. The way things go (for those fields I observed in Molecular Biology) • Field emerges • Scattered ecosystem of academic specialist databases appears • Field matures • Efforts on open data formats, (MI-) standards, happen • Long-term maintained databases by large data providers are founded (at NCBI, EBI, DDBJ, …) • Global data exchange network emerge
- 21. Experimental Repository Reference Layer Chemistry Spectroscopy Biology AnalysisTools Primary Literature Primary data and Meta-Data, Spectra, Protocols, Synopses, ... MetaboLights Database at the EBI
- 22. 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
- 23. 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
- 24. 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
- 25. Data growth in EBI data repositories
- 26. Data growth in EBI data repositories 3-month doubling time for Metabolomics
- 27. 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
- 28. Funded through European Commission COSMOS Grant EC312941
- 29. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126.
- 30. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies
- 31. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Minimum Information Standards
- 32. Repository Entry
- 33. Repository Entry
- 34. Reference Layer
- 35. Reference Layer
- 36. Reference Layer 1000 species up from Spring 2016
- 40. 30 most annotated metabolomes in MetaboLights
- 41. Metabolome sizes in MetaboLights on a log scale
- 42. Number of Studies in MetaboLights per Species
- 45. Lessons learned from this excursion into bioinformatics • You can get people into depositing data by convincing publishers to require it. • This is easier once it became a community meme. • Publishers, learned societies and funders actually want this to happen, but are afraid. • If one starts, others follow. • It takes about six years to get there, once others have done it.
- 47. Thanks for your attention