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The time is right to focus on a model organism database

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Following the success of global efforts to exchange genomic and other biomedical data, we have now witnessed the emergence of global databases in metabolomics. The MetaboLights database, the first general purpose, cross-species, cross-application database in metabolomics, became the fastest growing data repository at the EMBL-EBI in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights through user submissions. User submission of data to public repositories such as MetaboLights are now not only encouraged by publishers and funders but can now also directly benefit the publication record of a scientist by describing the published dataset in a data publication in journals such as Nature Scientific Data.

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The time is right to focus on a model organism database

  1. 1. The Time is Right to Focus on a Model Organism Metabolome Database Christoph Steinbeck European Bioinformatics Institute (EMBL-EBI)
  2. 2. •8.7 mio eukaryotic species on earth (+- 1.3mio)
  3. 3. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified
  4. 4. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
  5. 5. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
  6. 6. •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?
  7. 7. •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?
  8. 8. Metabolomics has taken off world-wide
  9. 9. 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)
  10. 10. Species Metabolomes are being assembled on the fly right now through data sharing in Metabolomics
  11. 11. Experimental Repository Reference Layer Chemistry Spectroscopy Biology AnalysisTools Primary Literature Primary data and Meta-Data, Spectra, Protocols, Synopses, ... MetaboLights Database at the EBI
  12. 12. 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
  13. 13. 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
  14. 14. 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
  15. 15. Data growth in EBI data repositories
  16. 16. Data growth in EBI data repositories 3-month doubling time for Metabolomics
  17. 17. 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
  18. 18. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126.
  19. 19. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies
  20. 20. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Minimum Information Standards
  21. 21. Repository Entry
  22. 22. Repository Entry
  23. 23. Reference Layer
  24. 24. 7 most annotated metabolomes in MetaboLights
  25. 25. 30 most annotated metabolomes in MetaboLights
  26. 26. 1600 metabolome sizes in MetaboLights on a log scale
  27. 27. Number of Studies in MetaboLights per Species
  28. 28. Share private prepublication studies with reviewers and other trusted parties. Biocrates XML with raw data is annotated and uploaded
  29. 29. A Case for Deep Metabolome Annotation
  30. 30. A Case for Deep Metabolome Annotation Help building species metabolomes •Submit your metabolomics study to MetaboLights •Submit data publications (e.g. to Scientific Data) •Be highly cited :)
  31. 31. Slides at https://www.slideshare.net/csteinbeck Funding
  32. 32. Thanks for your attention
  33. 33. Metabolights-help@ebi.ac.uk Thank you!

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