Building an efficient infrastructure, standards and data flow for metabolomics
0 likes186 views
Christoph Steinbeck from the European Bioinformatics Institute discusses developing efficient infrastructure, standards, and data flow for metabolomics. Metabolomics measures small molecule metabolites in organisms and generates large amounts of data. The MetaboLights database was created to share metabolomics data openly. It is growing rapidly with a doubling time of 3 months for metabolomics data. Efforts are underway to build standardized reference data through projects like COSMOS and MetabolomeXchange. While genomes of thousands of species have been sequenced, far fewer complete metabolomes exist. The talk advocates for focused efforts to map metabolites and build quantitative models of well-studied model organisms' metabolomes.
![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](https://image.slidesharecdn.com/buildinganefficientinfrastructureformetabolomics-bfr-berlin-28-11-2016-161128123003/85/Building-an-efficient-infrastructure-standards-and-data-flow-for-metabolomics-8-320.jpg)
Building an efficient infrastructure, standards and data flow for metabolomics
- 1. Developing an Efficient Infrastructure, Standards and Data-Flow for Metabolomics Christoph Steinbeck European Bioinformatics Institute (EMBL-EBI)
- 2. Developing an Efficient Infrastructure, Standards and Data-Flow for Metabolomics Christoph Steinbeck European Bioinformatics Institute (EMBL-EBI) Slides on http://www.slideshare.net/csteinbeck
- 7. The European Molecular Biology Laboratory (EMBL) A basic research institute funded by public research monies from 20 member states.
- 8. 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
- 11. Reaction times following external change • Genetics (decades, centuries…) • Epigenetics (days, month, years,…) • Gene Expression (hours) • Metabolism (seconds)
- 12. The Metabolome is the most accessible and dynamically changing Molecular Phenotype
- 13. Metabolites: Small molecules in biological organisms
- 14. Metabolomics Measures occurrence and concentrations of many small molecules (metabolites) in an organism at once.
- 15. Nuclear Magnetic Resonance (NMR) Mass Spec Metabolomics uses a wide-range of analytical techniques
- 16. Phenome Centres popping up all over the world • London • Birmingham • Shanghai • NIH RCMRCs • …
- 18. > 100,000 patient samples / year > Several PetaBytes/year => ExaBytes of human data at moderate scale-up
- 19. How do you make sense of all that data?
- 20. Share them - Free and Open
- 21. MetaboLights http://www.ebi.ac.uk/metabolights open-access, cross-species, cross-application, long-term supported Salek, R.M., Haug, K. and Steinbeck, C. (2013) Dissemination of metabolomics results: role of MetaboLights and COSMOS. Gigascience, 2:8.
- 22. MetaboLights Database Experimental Repository Reference Layer Chemistry Spectroscopy Biology AnalysisTools Primary Literature Primary data and Meta-Data, Spectra, Protocols, Synopses, ...
- 26. Data growth in EBI data repositories
- 27. Data growth in EBI data repositories 3-month doubling time for Metabolomics
- 28. 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
- 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
- 40. COSMOS COrdination of Standards in MetabolOmicS European FP7 coordination action coordinated by us at EMBL-EBI, Hinxton, Cambridge • Create missing standards & formats • Define workflows for dissemination • Create world-wide data network
- 41. MetabolomeXchange 2014 • Global network for exchange and discoverability of metabolomics data • Includes study as well as reference data
- 46. •8.7 mio eukaryotic species on earth (+- 1.3mio)
- 47. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified
- 48. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 49. •8.7 mio eukaryotic species on earth (+- 1.3mio) •1.2 mio species identified and classified •3000 - 4000 complete species genomes sequenced
- 50. •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?
- 51. •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?
- 52. Typical total ion chromatogram of serum from a healthy subject. Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, et al. (2011) The Human Serum Metabolome. PLoS ONE 6(2): e16957. doi:10.1371/ journal.pone.0016957 http://journals.plos.org/plosone/article?id=info:doi/10.1371/journal.pone.0016957
- 53. There are known knowns; there are things we know we know. We also know there are known unknowns; that is to say, we know there are some things we do not know. But there are also unknown unknowns – the ones we don’t know we don’t know. —United States Secretary of Defense, Donald Rumsfeld
- 54. 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)
- 55. Species Metabolomes are being assembled on the fly right now through data sharing in Metabolomics
- 56. Repository Entry
- 57. Repository Entry
- 58. Reference Layer
- 62. 7 most annotated metabolomes in MetaboLights
- 65. Funding and Collaborators UK Research Councils (BBSRC, MRC) European Commission