eScience Resources for the Chemistry Community from the Royal Society of Chemistry


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Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of the solutions that it helps to enable. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.

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eScience Resources for the Chemistry Community from the Royal Society of Chemistry

  1. 1. eScience Resources for the Chemistry Community from the Royal Society of Chemistry Antony Williams NCSU, College of Textiles October 2nd 2013
  2. 2. We Have …Too Much Data!!!
  3. 3. The World of Online Chemistry • Property databases • Compound aggregators • Screening assay results • Scientific publications • Encyclopedic articles (Wikipedia) • Metabolic pathway databases • ADME/Tox data – eTOX for example • Blogs/Wikis and Open Notebook Science
  4. 4. e-Science and Primary Data • How much data generated in a lab, that COULD go public, is lost forever?
  5. 5. e-Science and Primary Data • How much data generated in a lab, that COULD go public, is lost forever? • Public Domain reference databases of value? – Syntheses – Properties – Spectra – CIFs – Images
  6. 6. e-Science and Primary Data • How much data generated in a lab, that COULD go public, is lost forever? • Public Domain reference databases of value? – Syntheses – Properties – Spectra – CIFs – Images • Much of chemistry is chemical structure-based – where and how could we host these data?
  7. 7. RSC’s ChemSpider
  8. 8. ChemSpider • >29 million unique chemicals from >500 data sources • Focus on improving data quality, enhancing functionality, integrating and enabling
  9. 9. Crowdsourced “Annotations” • Users can add – Descriptions/Syntheses/Commentaries – Links to PubMed articles – Links to articles via DOIs – Add spectral data – Add Crystallographic Information Files – Add photos – Add MP3 files – Add Videos
  10. 10. Spectra
  11. 11. Chemistry Data online are messy • We have inherited errors • All public compound databases have errors • “Incorrect” structures – assertions, timelines etc • “Incorrect” names associated with structures • Properties • Links • Publications • ENORMOUS CHALLENGE
  12. 12. Crowdsourced Curation • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
  13. 13. Search “Vitamin H”
  14. 14. “Curate” Identifiers
  15. 15. “Curate” Identifiers
  16. 16. “Curate” Identifiers
  17. 17. Validated Name-Structure Dictionaries • Chemical name dictionaries are used for: • Text-mining (publications, patents) – Used to index PubMed and link to Google Patents • Linking to other databases – think Biology! – When structures are not available drug names link • Searching the web – Names link to structures link to InChIs
  18. 18. I want to know about “Vincristine”
  19. 19. Vincristine: Identifiers and Properties
  20. 20. Vincristine: Vendors and Sources Linked by Structure
  21. 21. Vincristine: Patents Linked by Name
  22. 22. Vincristine: Articles Linked by Name
  23. 23. Semantic Mark-up of Articles
  24. 24. Linking Names to Structures
  25. 25. The InChI Identifier
  26. 26. InChIStrings Hash to InChIKeys
  27. 27. Vancomycin – Search the Internet
  28. 28. Vancomycin Search Molecular SKELETON Search Full Molecule
  29. 29. Full Skeleton Search: 104 Hits
  30. 30. Full Molecule Search: 4 Hits
  31. 31. ChemSpider Resources for Chemistry
  32. 32. Some usage statistics • ca. 200 visitors at any one time, ~30,000 visits per day • Mar 4-Apr 3, 2013 – Visits = 731,656 – Unique Visitors = 527,008 • Independent servers to support other projects
  33. 33. Publications - a summary of work • Scientific publications are a summary of work – Is all work reported? – How much science is lost to pruning? – What of value sits in notebooks and is lost? • How much data is lost? – How many compounds never reported? – How many syntheses fail or succeed? – How many characterization measurements?
  34. 34. About Me…as a Chemist • I’ve performed a few dozen chemical syntheses • I’ve run thousands of analytical spectra • I’ve generated thousands of NMR assignments • I’ve probably published <5% of all work • Most of it has been lost • But things can be different today…. • But it still needs to be associated with me…
  35. 35. Micropublishing Syntheses
  36. 36. ChemSpider SyntheticPages
  37. 37. Olympicene
  38. 38. So you Want a Profile???
  39. 39. Interactive Data
  40. 40. Rewards and Recognition Congratulations! Your 1st CSSP article has been published. Philosopher Lao Tzu said “A journey of a thousand miles begins with a single step”. In the same way we hope that this will be the first of many submissions that you make to CSSP. The First Step badge is awarded when a user submits (& has published) their 1st CSSP article.
  41. 41. Integrate to instruments and software • Integration to analytical instrumentation vendors already in place – Agilent, Bruker, Thermo, Waters • Also, Cheminformatics vendors link to ChemSpider – Accelrys, ACD/Labs, ChemAxon, iChemLabs, and…
  42. 42. PharmaSea • Dereplication via ChemSpider • Segregation of natural products datasets • Analytical data algorithms & integration – Mass spec searching – predicted fragmentation – NMR feature searching – NMR prediction – Computer-assisted structure elucidation
  43. 43. It is so difficult to navigate… What’s the structure? What’s the structure? Are they in our file? Are they in our file? What’s similar? What’s similar? What’s the target? What’s the target?Pharmacology data? Pharmacology data? Known Pathways? Known Pathways? Working On Now? Working On Now?Connections to disease? Connections to disease? Expressed in right cell type? Expressed in right cell type? Competitors?Competitors? IP?IP?
  44. 44. • 3-year Innovative Medicines Initiative project • Integrating chemistry and biology data using semantic web technologies • Open source code, open data and open standards • Academics, Pharma companies, Publishers….
  45. 45. ChemSpider Contributions • The host of the chemistry services – Supplier of “standardized” chemical data files – Chemistry searching (structure, substructure etc) – Curator and data quality checking • We built the Open PHACTS chemical registration system
  46. 46. Open Source Drug Discovery
  47. 47. Chemical Database Service • National Chemical Database Service for UK Academics • Integrating Commercial Databases and Services • Chemicals, analytical data, prediction algorithms • Development of data repository
  48. 48. Community Repository for Data • Funding agencies encourage sharing of data • Increasing availability of “Open Data” • Institutional repositories no specific domain support • Develop a community repository for chemistry data – private, public, embargoed • Provides data to develop models and algorithms
  49. 49. Community Repository for Data • Automated depositions of data • DOI’ed data objects for citation purposes • A database of reference data, but validated by the community • National services feeding the repository – crystallography, mass spectrometry • Integrate to blogging tools for chemistry • Integrate to Electronic Lab Notebooks as feeds
  50. 50. Model Building with Community Data • Community data as a basis of model building – Consume data from available databases, community data, new publications and build predictive algorithms for the community – How many algorithms are reported and lost? How much repeat work is done in the domain of algorithmic development?
  51. 51. Inside our Publication Archive • How much data is in the archive, in the publications and in the supplementary info? – How many compounds for ChemSpider? – How many syntheses for ChemSpider reactions? – How many characterization measurements? • Property Data • Spectral Data • Graphs and charts to be used for modeling?
  52. 52. What if we could capture it all? Digitally Enhancing the RSC Archive
  53. 53. Start with data in publications
  54. 54. Turn “Figures” Into Data
  55. 55. ChemSpider Reactions • Starting with data from CSSP, MOS and CCR • Will cover reactions extracted from: • Patents • RSC journal articles and ESI
  56. 56. E-Lab Notebooks • Integration between ELNs and: • ChemSpider • ChemSpider Reactions • Chemistry Data Repository
  57. 57. Internet Data The Future Commercial Software Pre-competitive Data Open Science Open Data Publishers Educators Open Databases Chemical Vendors Small organic molecules Undefined materials Organometallics Nanomaterials Polymers Minerals Particle bound Links to Biologicals
  58. 58. The Future of Chemistry on the Web? • Public compound databases federate & build a linked environment of validated data! • Data validation needs are not ignored • Publishers layer on information to make publications discoverable • Open Data proliferate • The “Semantic Web” will continue to develop…
  59. 59. Thank you Email: Twitter: @ChemConnector Personal Blog: SLIDES: