Overview of open resources to support automated structure verification and elucidation
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The document discusses the importance of open resources and databases for automated structure verification and elucidation, emphasizing the need for public access to data in standardized formats. It highlights current limitations in data sharing practices and advocates for improved integration of spectral data and algorithms in scientific research. The presentation concludes by acknowledging the ongoing growth of online data and the critical role of data quality and openness in advancing research efforts.
Overview of open resources to support automated structure verification and elucidation
- 1. Overview of open resources to support automated structure verification and elucidation Antony Williams1 and Emma Schymanski2 1. National Center for Computational Toxicology, US EPA, Research Triangle Park, Durham, NC, USA. 2. Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Luxembourg. March 2018 ACS Spring Meeting, New Orleans http://www.orcid.org/0000-0002-2668-4821 The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA
- 2. Today’s Session • Our focus for the session: – Access to data to support automated structure verification and elucidation – NMR and MS – Data quality, curation and validation – and a call to action – OPENness is here – Open Access, Data, Source – Data standards – we already have them and there are more coming – Vendors and scientists providing and using available data – There are tools USING these data for Structure Elucidation – Cannot be an exhaustive review…but at least a good start 1
- 3. An Ideal Scenario… • All published structures and spectra will be available from all published articles for repurposing and reuse in standard formats (preferably not necessarily Open!) • Scientists are building open approaches – MS fragmentation – NMR shift prediction – Structure generators – Computer-Assisted Structure Elucidation (CASE) • Are we there yet??? 2
- 4. Publishers sharing data • We have achieved ideal scenario right? • No – PDF figures in Supplementary Info is still the default • There is a need for public databases of spectral data. There ARE some out there. • Analogous to Wikipedia, we are primarily consumers rather than contributors… 3
- 5. Sites sharing data • There are many sites that “share” spectral data. Generally in non-open formats • There are rich resources • Cannot easily be used to serve automated structure verification and elucidation 4
- 6. PubChem – Spectral Links 5
- 7. PubChem - Spectral Links 6
- 8. Spectral Links to Partial Data 7
- 9. SDBS – Free Not Open 8
- 10. SDBS – Free Not Open 9
- 11. SDBS – Free Not Open 10
- 12. ChemSpider 11
- 13. ChemSpider 12
- 14. ChemSpider 13
- 17. Focused Databases • Focused databases – Compiled focused databases of Open Data are preferable – Spectral data for structure verification and elucidation – Open Mass Spec Data especially useful (Emma’s talks!) – Data can be brought in-house and integrated – Algorithms can be derived – e.g. NMR shift prediction 16
- 21. Open Resources • Open Databases offer more value – Bring the data in-house, integrate, link – Ingest and train algorithms 20
- 26. Integrating Data and Services • Integration: – Use simple URL linking for navigation – Provide simple services for real time prediction 25
- 27. Example Integration via the CompTox Chemistry Dashboard 26
- 29. Link Access 28
- 30. 29
- 31. Open Data For Bulk Predictions 30 • Open Data for apps – Structures – CAS Registry Numbers – Names – Formulae – Mass • iOS app including predicted C13 NMR
- 33. Mass and CNMR Searching 32
- 34. Important Standards in our efforts • Structures – Molfile, SDF file, InChIs (standard and non-standard) • NMR – JCAMP and all its variants • MS – mz(X)ML, MSP (and all its variants), MGF, MassBank 33
- 35. There are more coming 34
- 36. Conclusion • The abundance of online data continues to grow • There are “integrated data”, there are databases, there are online tools, there are mobile apps • Data Quality is critical and OPENness is enabling – Open Data – Open Standards – Open Source • The rest of the day will expand on these efforts… 35
- 37. Contact Antony Williams US EPA Office of Research and Development National Center for Computational Toxicology (NCCT) Williams.Antony@epa.gov ORCID: https://orcid.org/0000-0002-2668-4821 36