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RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
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RSC ChemSpider – Building An Internet Based Community For Chemists

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This is a general presentation about our efforts to build an internet based community for chemists using ChemSpider. A general overview of data quality online, crowdsourced deposition and curation and …

This is a general presentation about our efforts to build an internet based community for chemists using ChemSpider. A general overview of data quality online, crowdsourced deposition and curation and our progress to deliver a solution to the community for resourcing data.

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  • 1. RSC ChemSpider – Building an Internet Based Community for Chemists<br />
  • 2. Where is chemistry online?<br />Encyclopedic articles (Wikipedia)<br />Chemical vendor databases<br />Metabolic pathway databases<br />Property databases<br />Patents with chemical structures<br />Drug Discovery data<br />Scientific publications <br />Compound aggregators<br />Blogs/Wikis and Open Notebook Science<br />
  • 3. Chemistry on the Internet TODAY<br />Chemistry searches are generally limited to text-based searches across the internet<br />Poor quality and little curation/validation work<br />Too many searches required to resource data<br />
  • 4. What do humans want?<br />media.obsessable.com<br />As few interfaces as possible<br />
  • 5. Chemistry on the Internet FUTURE<br />Search by chemical structure and substructure<br />Chemistry articles indexed and searchable<br />Reduced number of searches to find data<br />Data are integrated – compounds, vendors, syntheses, data, publications and patents<br />
  • 6. For Synthesis…TotallySynthetic.com<br />
  • 7. Org Prep Daily (Blog)<br />
  • 8. Lots of “Public Compound” Databases<br />PubChem<br />Drugbank<br />ChEBI/ChEMBL<br />KEGG<br />LipidMAPs<br />ChemIDPlus<br />eMolecules<br />ZINC<br />Lots of chemical vendors<br />ChemSpider<br />
  • 9. Where Would You look? What Do You Trust?<br />
  • 10. Linked Data on the Web<br />Taken from: Rafael Sidis’ Blog<br />
  • 11. What is a compound?<br />
  • 12. What is ChemSpider?<br />ChemSpider is:<br />Building a Structure Centric Community for Chemists<br />&gt;23 million compounds, &gt;300 data sources<br />A deposition and curation platform<br />A publishing platform for the community<br />Grows daily – more depositions, more links, more data sources<br />
  • 13. How Was ChemSpider Built?<br />ChemSpider was a “hobby project” <br />Housed in a basement and running off three servers – one bought, two built<br />Sensitive to weather and power stability<br />Went live at ACS Spring 2007 in Chicago<br />
  • 14. Search Cholesterol<br />
  • 15. Search Cholesterol<br />
  • 16. Search Cholesterol<br />
  • 17. Search Cholesterol<br />
  • 18. Search Cholesterol<br />
  • 19. Linked across the internet<br />
  • 20. Kyoto Encyclopedia of Genes and Genomes <br />
  • 21. Link off a structure in ChemSpider<br />Chemical suppliers<br />Other publications<br />Analytical Data<br />Related Reactions<br />Wikipedia<br />Patents<br />“Everything”<br />
  • 22. Links to Patents based on structure<br />
  • 23. Clickthrough to Patents<br />
  • 24. Articles Linked<br />
  • 25. Answering Questions for Chemists<br />Questions a chemist might ask…<br />What is the melting point of n-butanol? <br />What is the chemical structure of Xanax?<br />Chemically, what is phenolphthalein?<br />What are the stereocenters of cholesterol?<br />Where can I find publications about xylene?<br />What are the different trade names for Ketoconazole?<br />What is the NMR spectrum of Aspirin?<br />What are the safety handling issues for Thymol Blue?<br />
  • 26. Complex Data and Information<br />
  • 27. ChemSpider is a structure-centric hub<br />ChemSpider aggregates and links out across the internet<br />Data aggregate based on “structures and links”<br />What defines a chemical compound?<br />
  • 28. What is a compound?<br />
  • 29. Question Everything online: www.dhmo.org<br />
  • 30. Di-Hydrogen Monoxide<br />2H<br />
  • 31. Di-HydrogenMonoxide<br />2H + 1O<br />
  • 32. Di-Hydrogen Monoxide<br />H2O<br />
  • 33. Di-Hydrogen Monoxide<br />H2O<br />Water<br />
  • 34. It’s all on Wikipedia…<br />
  • 35. It’s all on Wikipedia…<br />
  • 36. Chemistry on The Internet Is Messy<br />
  • 37. It’s Methane…<br />
  • 38. What’s Methane?<br />
  • 39. What’s Methane?<br />
  • 40. What ELSE is Methane???<br />
  • 41. PubChem<br />
  • 42. Truly “I Love You”<br />
  • 43. Chemistry is REALLY Messy<br />
  • 44. Vancomycin<br />Who will curate?<br />How would you clean such a large dataset?<br />Assertions!!!<br />
  • 45. Vancomycin<br />Who will curate?<br />How would you clean such a large dataset?<br />
  • 46. Vancomycin on ChemSpider 1 compound – 3 days <br />
  • 47. The EXPERTS must get it right?!<br />
  • 48. Wikipedia, C&E News, PubChem<br />C&E News (from ACS)<br />
  • 49. What About Digitonin?<br />
  • 50. CAS as an authority<br />
  • 51. The Blogging Community Participate <br />
  • 52. The FDA’s DailyMed<br />
  • 53. Structures on DailyMed<br />
  • 54. Lack of Stereochemisty<br />
  • 55. Incorrect Structures<br />
  • 56. Wow!<br />
  • 57. The InChI Identifier<br />
  • 58. Multiple Layers<br />
  • 59. InChIStrings Hash to InChIKeys<br />
  • 60. InChIs for Taxol<br />
  • 61. Back to Taxol<br />DrugBank: RCINICONZNJXQF-CLDWUXIMDD<br />ChEBI: RCINICONZNJXQF-GXKQXQCDDN <br />Wikipedia: RCINICONZNJXQF-MZXODVADBJ<br />Which one is correct???<br />
  • 62. InChIKeys for Taxol<br />DrugBank: RCINICONZNJXQF-CLDWUXIMDD<br />ChEBI: RCINICONZNJXQF-GXKQXQCDDN <br />Wikipedia: RCINICONZNJXQF-MZXODVADBJ<br />ChEBI and Wikipedia are the SAME structure<br />Drugbank is a DIFFERENT structure – ONE stereocenter<br />
  • 63. Does one stereocenter matter?<br />
  • 64. Does one stereocenter matter?<br />Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon <br />
  • 65. Does one stereocenter matter?<br /><ul><li>Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon </li></li></ul><li>Building a Structure Centric Community for Chemists<br />
  • 66. Assertion and Chemical Entities<br />Who says what Taxol is?<br />What is the “timeline” for a molecule?<br />How do we clean up the Public data?<br />The Quality source is Chemical Abstracts Service…<br />
  • 67. ChemSpider Searches<br />
  • 68. ChemSpider Searches<br />
  • 69. ChemSpider Complex Searches<br />
  • 70. Vancomycin – Search the Internet<br />
  • 71. Full Molecule Search: 4 Hits<br />
  • 72. Full Skeleton Search: 104 Hits<br />
  • 73. The InChI “Resolver”<br />
  • 74. Citizen Scientists<br />
  • 75. Crowd-sourcing Chemistry Curation<br />Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate<br />
  • 76. Building a Structure Centric Community for Chemists<br />Multi-level Curation and Approval<br />
  • 77. Citizens as Data Sources <br />
  • 78.
  • 79. Entity-Extraction, Mark-up, Annotate<br />
  • 80. Success Depends on Dictionaries<br />
  • 81. Project Prospect<br />
  • 82. ChemMantis and CJOC<br />
  • 83. Name-Structure Pairs<br />
  • 84. Species – linked to Wikipedia<br />
  • 85. Semantic Linking of Structures<br />What would you want to link off a structure?<br />Chemical suppliers<br />Other publications<br />Analytical Data<br />Related Reactions<br />Wikipedia<br />Patents<br />“Everything”<br />
  • 86. ChemSpider Everywhere<br />Linked from Wikipedia<br />Linked from Open Notebook Science sites using EMBED<br />Linked from Blogs using Structure/Spectra EMBED<br />Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets<br />Integrated to software offerings from Thermo, Waters, Agilent, Bruker<br />
  • 87. ChemSpider Everywhere : Embed<br />
  • 88. ChemSpider Everywhere:What do computers want?<br />Web services<br />flickr.com/photos/microcosmos<br />
  • 89. ChemSpider Everywhere: Spectral Game<br />
  • 90. ChemSpider EverywhereCrowdsourced Curation of Spectra<br />
  • 91. ChemSpider EverywhereChemMobi<br />
  • 92. There are always gaps...<br />What ChemSpider doesn’t deal with yet...<br />Markush structures and other “non-defineds”<br />Materials<br />Minerals<br />Polymers<br />Biological macromolecules<br />
  • 93. What’s next?<br />Continue the curation effort and keep cleaning<br />Finish depositions – millions left to deposit <br />Layer on RDF to allow the semantic web to benefit from our efforts<br />Integrate RSC content – a massive archive!<br />Integrate RSC publishing workflows and databases<br />
  • 94. Thank you<br />antony.williams@chemspider.com<br />Twitter: ChemSpiderman<br />www.chemspider.com/blog<br />SLIDES: www.slideshare.net/AntonyWilliams<br />

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