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Building a Model Organism Metabolome Database
The document discusses the establishment and growth of a metabolome database at the European Bioinformatics Institute, which aims to archive and facilitate the sharing of metabolomic data from various laboratories worldwide. It highlights the significant increase in data over time and the importance of collaboration in the field of metabolomics. The document emphasizes the role of publishers and community support in promoting data sharing and establishing standards in bioinformatics.
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Building a Model Organism Metabolome Database
- 1. Building a Model Organism Metabolome Database ChristophSteinbeck European Bioinformatics Institute, Cambridge, UK Friedrich-Schiller-University, Jena, Germany
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- 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 eukaryoticspecies on earth (+- 1.3mio)
- 10. •8.7 mio eukaryoticspecies on earth (+- 1.3mio) •1.2 mio species identified and classified
- 11. •8.7 mio eukaryoticspecies on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 12. •8.7 mio eukaryoticspecies on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 13. •8.7 mio eukaryoticspecies 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 eukaryoticspecies 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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- 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 HowLittle We Know (2008 vs 2016) 80,000 200,000 2,000,000
- 19. Metabolomics has taken offworld-wide
- 20. The way thingsgo (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 ChemistrySpectroscopy Biology AnalysisTools Primary Literature Primary data and Meta-Data, Spectra, Protocols, Synopses, ... MetaboLights Database at the EBI
- 22. MetaboLights Database atthe 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 atthe 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 atthe 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 inEBI data repositories
- 26. Data growth inEBI data repositories 3-month doubling time for Metabolomics
- 27. Data growth inEBI 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 EuropeanCommission COSMOS Grant EC312941
- 29. Sansone,… Steinbeck etal. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126.
- 30. Sansone,… Steinbeck etal. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies
- 31. Sansone,… Steinbeck etal. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Minimum Information Standards
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- 36. Reference Layer 1000 speciesup from Spring 2016
- 40. 30 most annotated metabolomesin MetaboLights
- 41. Metabolome sizes in MetaboLightson a log scale
- 42. Number of Studiesin MetaboLights per Species
- 45. Lessons learned fromthis 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.
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- 47. Thanks for yourattention