Publication of raw and curated NMR spectroscopic data for organic molecules
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The document discusses nuclear magnetic resonance (NMR) spectroscopy and the need for sharing raw NMR data. It describes NMRReData as a machine-readable representation for linking NMR spectral data to chemical structures. Benefits of NMRReData include improved data quality, easier data sharing and storage, and validation of results. The document also calls for building a stable, open archive with community standards for submitting raw NMR data and metadata. Existing frameworks could support such an archive by handling submissions and allowing search/visualization of NMR data.
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Publication of raw and curated NMR spectroscopic data for organic molecules
- 2. Christoph Steinbeck Publication of raw and curated NMR spectroscopic data for organic molecules https://slideshare.net/csteinbeck
- 4. 😀
- 5. Nuclear Magnetic Resonance (NMR) in Synthetic Organic Chemistry Source: https://www.beilstein-journals.org/bjoc/articles/14/188 Provides marginal evidence in experimental section that the reported structure is what we say it is.
- 6. Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 7. Chemical Name Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 8. Chemical Class Chemical Name Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 9. Chemical Class Chemical Name Biol. Species Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 10. Chemical Class Chemical Name Biol. Species Biol.Activity Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 11. Chemical Class Chemical Name Biol. Species Biol.Activity Phys.chem. data Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 12. Chemical Class Chemical Name Biol. Species Biol.Activity Structure Diagram Phys.chem. data Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 13. Chemical Class Chemical Name Biol. Species Biol.Activity Structure Diagram Phys.chem. data Atom Numbers Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 14. Chemical Class Chemical Name Biol. Species Biol.Activity Structure Diagram Phys.chem. data Atom Numbers Spectral data Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Hoang, V. D. et al., Phytochemistry 59, 325–329 (2002).
- 15. Nuclear Magnetic Resonance (NMR) in Natural Products Chemistry Liu, F. et al., J. Nat. Prod., doi:10.1021/acs.jnatprod.7b01074 Image (!) from the supplemental information of Nat. Prod., 2018, 81 (7), pp 1553–1560
- 17. Research Data Sharing is becoming the norm … •… rather than the exception •but some disciplines are a little more behind than others … © https://matheplanet.com
- 18. Why do we archive, curate and disseminate (raw) research data? •Data re-use (including data use, reanalysis and repurposing) •Reproduction of scientific results • For this we actually need to share the computational workflow for processing the data as well (see http:// www.researchobject.org/) •Validation of methods
- 19. Why people do not share data • Fear of not being able to generate enough publications from their data • Fear of being scooped by other researchers (“Research Parasites”) • Fear that one’s own study is not replicable • Fear to expose badly managed, flawed or inconsistent data • Patient confidentiality • Technical reasons Smith, R. & Roberts, I. F1000Research 5, 781 (2016).
- 23. What is NMReData? Machine-Readable Representation
- 24. What is NMReData? Machine-Readable Representation based on industry standard format
- 25. What is NMReData? Machine-Readable Representation of chemical Structure based on industry standard format
- 26. What is NMReData? Machine-Readable Representation of chemical Structure and assigned NMR Data based on industry standard format
- 27. What is NMReData? Machine-Readable Representation of chemical Structure and assigned NMR Data based on industry standard format linked to the raw NMR Data
- 28. Why NMReData?
- 29. Why NMReData? • Improved quality of the NMR data for the community
- 30. Why NMReData? • Improved quality of the NMR data for the community • Straightforward inclusion of NMR data in reports and articles
- 31. Why NMReData? • Improved quality of the NMR data for the community • Straightforward inclusion of NMR data in reports and articles • Simplified referee work
- 32. Why NMReData? • Improved quality of the NMR data for the community • Straightforward inclusion of NMR data in reports and articles • Simplified referee work • Compatibility with electronic storage in databases
- 33. Why NMReData? • Improved quality of the NMR data for the community • Straightforward inclusion of NMR data in reports and articles • Simplified referee work • Compatibility with electronic storage in databases • Easier comparison of dataset
- 34. Why NMReData? • Improved quality of the NMR data for the community • Straightforward inclusion of NMR data in reports and articles • Simplified referee work • Compatibility with electronic storage in databases • Easier comparison of dataset • Improved searchability of NMR data
- 35. Why NMReData? • Improved quality of the NMR data for the community • Straightforward inclusion of NMR data in reports and articles • Simplified referee work • Compatibility with electronic storage in databases • Easier comparison of dataset • Improved searchability of NMR data • Automatic validation by computational means (e.g. CASE)
- 36. How is NMReData supported? • Support by major NMR software companies • Mag. Res. Chem. will require submission of NMReData • Leads to raw NMR data becoming regularly available • More journals needed - how about Journal of Natural Products? • I/O in NMRShiftDB2 available • Broad support by software ecosystem crucial for enduring success • For updates see http://www.nmredata.org/wiki/ Compatible_software
- 37. McAlpine, J. B. et al., Nat. Prod. Rep. 33, 1028 (2018).
- 38. McAlpine, J. B. et al., Nat. Prod. Rep. 33, 1028 (2018).
- 39. Why do we need a raw NMR Archive?
- 41. The Raw NMR Archive (…to be built)
- 42. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive
- 43. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements:
- 44. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc)
- 45. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc) • Community agreed Minimum Information Standard
- 46. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc) • Community agreed Minimum Information Standard • see https://fairsharing.org/ for examples, could be based on MIABE and MIBiG
- 47. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc) • Community agreed Minimum Information Standard • see https://fairsharing.org/ for examples, could be based on MIABE and MIBiG • Framework for handling submissions of raw data and meta-data
- 48. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc) • Community agreed Minimum Information Standard • see https://fairsharing.org/ for examples, could be based on MIABE and MIBiG • Framework for handling submissions of raw data and meta-data
- 49. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc) • Community agreed Minimum Information Standard • see https://fairsharing.org/ for examples, could be based on MIABE and MIBiG • Framework for handling submissions of raw data and meta-data • Ability to process, visualise and search 1D and 2D NMR data
- 50. The Raw NMR Archive (…to be built) • There is momentum for building a raw NMR data archive • Requirements: • Stable funding and operation (EBI, NCBI, ELIXIR node, etc) • Community agreed Minimum Information Standard • see https://fairsharing.org/ for examples, could be based on MIABE and MIBiG • Framework for handling submissions of raw data and meta-data • Ability to process, visualise and search 1D and 2D NMR data • Total openness and support for the FAIR principle
- 51. The Archive Framework Lives at https://www.ebi.ac.uk/metabolights or https://www.metabolights.org
- 52. The Archive Framework Lives at https://www.ebi.ac.uk/metabolights or https://www.metabolights.org I am not suggesting that this is it. I am just saying: Here is an open source framework with a scent of chemistry that does it all and it does it well
- 58. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. Data Submission to MetaboLights
- 59. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Data Submission to MetaboLights
- 60. Sansone,… Steinbeck et al. (2012) Toward interoperable bioscience data. Nature Genetics, 44, 121–126. ControlledVocabularies Ontologies Minimum Information Standards Data Submission to MetaboLights
- 61. ISA-Creator
- 65. Takeaways • Global momentum for sharing raw and curated NMR data • Open raw meta-data and data formats exist • Open frameworks for meta-data handling exist • Technical, chemistry-enabled archive frameworks available • Editors’ buy-in indispensable • It could start right now (Figshare->DOI->Manuscript)
- 66. Stop clinging to your precious … • We are still seeing a multitude of new, small databases popping up • All locked behind registration walls and web interfaces allowing only for accessing individual datasets My precious … and share your chemistry data!