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

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At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of ...

At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.

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

  • 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
  • 14. 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
  • 32. Depositions Gateway User Interface
  • 33. Document processing
  • 34. Depositions Gateway User Interface
  • 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