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ChemSpider as an integration hub for interlinked chemistry data
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ChemSpider as an integration hub for interlinked chemistry data


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The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical …

The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties, both experimental and predicted, together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation any chemist can contribute to both the sharing and validation of chemistry-related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. Toxicologists commonly wish to source data, either for reference purposes, to support the development of models or, when experimental data are not available, predicted data will suffice. This presentation will offer a perspective of the type and quality of chemistry data available today, our experiences of building the ChemSpider public compound database to link together chemistry on the internet and our efforts to both encourage and enable even greater integration and connectivity for chemistry data for the community.

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  • 1. ChemSpider as an Integration Hub for Interlinked Chemistry Data Antony Williams SETAC November 18th 2013
  • 2. How Much Data Online? • How much data regarding environmental toxicology and chemistry is online? • How can it all be mapped together?
  • 3. A Grand Challenge…. • Let’s map together all historical chemistry data and build systems to integrate new data • Let’s integrate chemistry, toxicology and biology data and add in disease data too • Lets model the data and see if we can extract new relationships – quantitative and qualitative • Let’s make it all available on the web
  • 4. What about this…. • We’re going to map the world • We’re going to take photos of as many places as we can and link them together • We’ll let people annotate and curate the map • Then let’s make it available free on the web • We’ll make it available for decision making • Put it on Mobile Devices, Give it Away
  • 5. 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
  • 6. How to Map Data Together • Download the structure representations and map together at the structure level • Integrate and mesh chemical names, chemical properties, analytical data • Carry URL links and retain external links to original data sets (assume no link decay) • It sounds easy….
  • 7. ChemSpider • Build a HUB connecting as many data sources as possible • NOT to harvest all data from each data source • Today we have >29 million unique chemicals from >500 data sources • Focus on improving data quality • Allow users to enhance, curate and annotate
  • 8. RSC’s ChemSpider
  • 9. Identifiers are very useful! But what when they are “closed”
  • 10. CAS Numbers Validation?
  • 11. Various Registration Numbers
  • 12. Mappings and Inconsistencies Imatinib Mesylate ChemSpider Drugbank PubChem
  • 13. The InChI Identifier
  • 14. InChIStrings Hash to InChIKeys
  • 15. Vancomycin – Search the Internet
  • 16. Vancomycin Search Molecular SKELETON Search Full Molecule
  • 17. Full Skeleton Search: 529 Hits
  • 18. Full Molecule Search: 294 Hits
  • 19. Historical Data for reference • As evidence that InChI is proliferating and data is improving: • Three years ago there were only 104 hits on the complete InChI online • Only 4 were correct
  • 20. What you might not know about Chemistry Databases on the Internet
  • 21. NCGC Pharma Collection
  • 22. NCGC Pharma Collection
  • 23. NCGC Pharma Collection
  • 24. PHYSPROP Database • The freely downloadable database under the EPI Suite prediction software • Very Basic filters suggest data quality issues
  • 25. The Stereochemistry challenge. 12500 chemicals with “missed” stereo
  • 26. NIST Webbook
  • 27. PubChem
  • 28. Patents
  • 29. Patents
  • 30. But Chemspider is curated right?
  • 31. Originally 15 compounds “called” Yohimbine 54 Skeletons for Yohimbine
  • 32. Crowdsourced Curation • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
  • 33. Search “Vitamin H”
  • 34. “Curate” Identifiers
  • 35. “Curate” Identifiers
  • 36. “Curate” Identifiers
  • 37. Chemical name dictionaries for: • Text-mining (publications, patents) • Used to index PubMed and link Google Patents • Linking to other databases – think Biology! • When structures are not available names link • Searching the web • Names link to structures link to InChIs
  • 38. I want to know about “Vincristine”
  • 39. Vincristine: Identifiers to link
  • 40. Vincristine: Vendors and Sources Linked by Structure
  • 41. Vincristine: Patents Linked by Name
  • 42. Vincristine: Articles Linked by Name
  • 43. What needs to happen? • Standards • Standardization of structures • More sharing of data – downloadable data collections for mapping, meshing and integration • InChI adoption • Collaboration • Stop reinventing the wheel • Share data, share efforts and speed the process
  • 44. Adopting Modified FDA Rules
  • 45. Nitro groups
  • 46. Salt and Ionic Bonds
  • 47. Ammonium salts
  • 48. What if we could capture it all? Digitally Enhancing the RSC Archive
  • 49. Start with data in publications
  • 50. Text Mining The N-(β-hydroxyethyl)-N-methyl-N'-(2-trifluoromethyl-1,3,4thiadiazol-5-yl)urea prepared in Example 6 , thionyl chloride ( 5 ml ) and benzene ( 50 ml ) were charged into a glass reaction vessel equipped with a mechanical stirrer, thermometer and reflux condenser. The reaction mixture was heated at reflux with stirring , for a period of about one-half hour. After this time the benzene and unreacted thionyl chloride were stripped from the reaction mixture under reduced pressure to yield the desired product N-(β-chloroethyl)-Nmethyl-N'-(2-trifluoromethyl-1,3,4-thiaidazol-5-yl)urea as a solid residue
  • 51. ChemSpider Reactions
  • 52. Turn “Figures” Into Data FIGURE EXTRACTED DATA
  • 53. Conclusions • There are some amazing online resources for environmental toxicology and chemistry already! • ChemSpider has an important role in quality data and linking resources • Crowdsourced deposition, validation and curation works • Standards are an important part of data linking • MORE collaboration and data sharing can benefit us all
  • 54. Thank you Email: Twitter: @ChemConnector Personal Blog: SLIDES: