The UK National Chemical Database Service – an integration of commercial and public chemistry services to support chemists in the United Kingdom

1. UK National Chemical Database Service: An integration of commercial and public chemistry services to support chemists in the United Kingdom Antony Williams, Valery Tkachenko and Richard Kidd ACS Dallas March 2014

2. UK Chemical Database Service • The National Chemical Database Service is for UK academics – see later for Rest of World

3. Vision for the Service PART 1 • Provide access to databases and services of interest to the academic community to serve their needs. Access to services to include: • Crystallography data – Organic and inorganic materials • Thermophysical data • Reactions Data including retrosynthetic analysis • Prediction technologies – name generation, physicochemical parameters, NMR prediction

4. Service Rollout • Many services are hosted in the cloud • Access through login/password, IP authentication or Shibboleth authentication • Lots of hard work in a very short time – so much thanks to all of the service providers • More providers stepped up to help – ChemAxon • Crystallography concern (understatement!)

5. Feedback from Community • Converted initial public negativity spike on Twitter pre-release to very positive feedback post-release • Training required – onsite training sessions organized • Available Chemicals Directory is big plus! • Concerns with Retrosynthetic Analysis tool

6. Usage • Majority of usage is for crystallography data – previous provider had same bias • Usage is increasing month-by-month • Still way-under used and in many cases low awareness

7. Vision for the Service PART 2 • Response to the call for proposals included our vision for a 21st Century data repository • At a time of Open Access, Open Data and funding agency requirement to make data public – build a data repository • Funding is split for licensing content and services (VAST MAJORITY) and some funding for research and development

8. An Initial “Vague” Vision Set • Manage “all” of the chemistry data associated with chemical substances • Data to be downloadable, reusable, interactive • Build a platform that enables the scientist • Data storage, validation, standardization and curation • Collaborative data sharing • Provide data platform that can enable and enhance publishing of scientific papers

9. Data Repository • Registration of chemical compounds • Deposition of chemical syntheses • Addition of analytical data • Integration to electronic notebooks • Rewards and recognition for data sharing • Document processing • Hosting of data as private, embargoed or public

10. What we will deliver for all data • Simple interfaces for uploading of data • Embeddable widgets and programming interfaces to utilize in in-house systems, ELNs • Automated harvesting approaches – sweeping directories for data • Data validation where possible

11. Input data pipeline Deposition Gateway Staging databases Compounds Reactions Spectra Materials Articles / CSSP Compounds Module Spectra Module Reactions Module Materials Module Textmining Module Module Web UI for unified depositions DropBox, Google Drive, SkyDrive, etc LabTroveand other templated data Documents API, FTP, etc Raw data Validated data Staging databases Alldatabases are sliced by data sources/data collections and havesimple security model where each data slice/sourceis private, public or embargoed

12. Compounds upload • Draw chemicals in the interface (Javascript editors – PC, Mac, Tablets, Phones) • Drag and drop of compounds • Automated generate of properties – Formulae, Mw, Mi, physchem properties • Metadata input forms • Bulk upload

13. Depositions Gateway User Interface

15. Chemical Validation and Standardization

16. Reactions • Hosting of reaction data – standard “document formats” – full flexibility but limiting – extraction of data from embedded objects • Encourage template formats – using ELNs for example, community agreed templates

17. Electronic Notebook Data • Development work integrating chemistry into the Southampton Labtrove notebook • Stoichiometry table development • Analytical data integration • “ChemTrove” rolled out to a small test group in January

18. Micropublishing Syntheses

19. ChemSpider SyntheticPages

20. Requirements • Community agreement on acceptable templates for CSSP/Reactions deposition • Data Model deposition based on mappings between template and CSSP model • Adoption of Labtrove interface for deposition

21. What we will deliver • Micropublishing platform for submission of • Protocols and Procedures • Reactions • Safety and Hazard data (LATER) • Template-based submissions of procedures • Matched to ELN submissions • Full details for user submission versus mapped submission into database

22. Reaction Deposition/Validation

23. Reaction Deposition/Validation

24. Spectral Data • Support for “structure identification” is a must – “greatest value” for reference and lookup • Support for data standards primarily – JCAMP, mzML, SPC • Want to support ASSIGNED data formats • Hold binary files but prefer standards – WHY?

25. Raw Spectral Data

26. 10 years from now… • Binary file formats generally need original data processing software to deal with them – from Bruker, Agilent, Jeol, Thermo, Waters, blah, blah, blah, blah,… • While we can store the original raw data files for posterity should we? This has been one focus for data repositories

27. This is way more useful

28. Processed data… Spectral searching is made possible Spectral matching is possible

29. This is what we really want…

30. Addition of Analytical Data • Spectral Container is in development using componentized widgets for display • NIST spectra converted into standardized JCAMP format for deposition - 296,103 spectra deposited • 10% of remaining NIST spectra need to be curated as there are obvious structure issues

31. Javascript viewer NMR, MS, IR

33. Document processing

35. User Interface Approach Compounds Reactions Spectra Materials Documents Compounds API Reactions API Spectra API Materials API Documents API Compounds Widgets Reactions Widgets Spectra Widgets Materials Widgets Documents Widgets Data tier Data access tier User interface components tier Analytical Laboratory application User interface tier (examples) Electronic Laboratory Notebook Paid 3rd party integrations (various platforms – SharePoint, Google, etc) Chemical Inventory application

36. User Interface Approach Compounds Reactions Spectra Materials Documents Compounds API Reactions API Spectra API Materials API Documents API Compounds Widgets Reactions Widgets Spectra Widgets Materials Widgets Documents Widgets Data tier Data access tier User interface components tier Analytical Laboratory application User interface tier (examples) Electronic Laboratory Notebook Paid 3rd party integrations (various platforms – SharePoint, Google, etc) Chemical Inventory application

37. Analytical Chemist Characterize Measure Search Store <<include>> <<include>> <<include>> Synthetic Chemist Search (synthetic procedure) Document (publish synthetic procedure) Retrosynthetic analysis

38. Medicinal Chemist Search (against database of properties) Source (find vendor) Analyse (cluster, dock, screen) Computational Chemist Search or Develop algorithm Store results Run calculations Synthesize Measure activity

39. Present activities for ACS Fall • Deposition process development of compounds, reactions and spectral data by end of Spring • FTP, DropBox, Web-upload, ELN integration • Compounds, Reactions, Spectral data search, display, download • Data sharing – private, public, collaborative • Metadata, metadata, metadata standards! • Open Sourcing Chemical Registry System including CVSP

40. UK Chemical Database Service • The National Chemical Database Service is for UK academics • What would be necessary to make this available for “Rest of World”, a single institution, an organization? • It’s not really technology…that’s scale out and can be handled • It’s negotiation with database providers, pricing, login/authentication, localization?

41. Acknowledgments • Jeremy Frey and Simon Coles, University of Southampton • Will Dichtel and Leah McEwan, Cornell University • Stuart Chalk, University of North Florida • Bob Hanson and Bob Lancashire, Jmol and JSpecView

42. Thank you Email: williamsa@rsc.org ORCID: 0000-0002-2668-4821 Twitter: @ChemConnector Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

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