ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd Sourced Databasing Platform for Chemistry

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There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle …

There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.
There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.

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  • 1. Building a Foundation for the Semantic Web by Hosting a Crowdsourced Databasing Platform for Chemistry
  • 2. What’s the Status of Chemistry online?
    • Encyclopedic articles (Wikipedia)
    • Chemical vendor databases
    • Metabolic pathway databases
    • Virtual Screening databases
    • Property databases
    • Screening assay results
    • Patents with chemical structures (IBM & SureChem)
    • ADME/Tox data
    • Scientific publications
    • Compound aggregators
    • Blogs/Wikis and Open Notebook Science
  • 3. For Synthesis…
  • 4. Org Prep Daily (Blog)
  • 5. Molbank (Open Access Journal)
  • 6. Synthetic Pages (Website)
  • 7. Encyclopedic Articles (Wikipedia)
  • 8. Lots of “Public Compound” Databases
    • PubChem
    • Drugbank
    • ChEBI/ChEMBL
    • KEGG
    • LipidMAPs
    • ChemIDPlus
    • eMolecules
    • ZINC
    • Lots of chemical vendors
    • ChemSpider
  • 9. Where Would You look? What Do You Trust?
  • 10. Linked Data on the Web Taken from: Rafael Sidis’ Blog
  • 11. Compounds and Identifiers
  • 12. Connecting Chemistry on the Web
    • Connections are made
      • actively by purposeful linking
      • via semantic web links (i.e. RDF and triple stores)
      • by integrating via identifiers (InChI, CAS #, names and web service look ups)
  • 13. Connections Can Lead Anywhere
  • 14. The FUTURE of Chemistry on the Web
    • The internet is searchable by chemical structure and substructure (e.g.Wikipedia, Google Scholar)
    • Chemistry articles are indexed and searchable by a free online service
    • Publicly funded research data can be shared and discussed in the Open, maybe as ONS?
    • There is structure based access to property data (ADME/Tox), spectra, clean name-structure dictionaries
  • 15. What is ChemSpider?
    • ChemSpider is:
      • Building a Structure Centric Community for Chemists
      • >20 million compounds, >200 data sources
      • A deposition and curation platform
      • A publishing platform for the community
      • Grows daily – more depositions, more links, more data sources
  • 16. Search Cholesterol
  • 17. Search Cholesterol
  • 18. Search Cholesterol
  • 19. Search Cholesterol
  • 20. Search Cholesterol
  • 21. Search Cholesterol
  • 22. Linked across the internet
  • 23. Kyoto Encyclopedia of Genes and Genomes
  • 24. Link off a structure in ChemSpider
      • Chemical suppliers
      • Other publications
      • Analytical Data
      • Related Reactions
      • Wikipedia
      • Patents
      • “ Everything”
  • 25. Links to Patents based on structure
  • 26. Clickthrough to Patent (SureChem)
  • 27. Pubmed Articles Linked
  • 28. Answering Questions for Chemists
    • Questions a chemist might ask…
      • What is the melting point of n-butanol?
      • What is the chemical structure of Xanax?
      • Chemically, what is phenolphthalein?
      • What are the stereocenters of cholesterol?
      • Where can I find publications about xylene?
      • What are the different trade names for Ketoconazole?
      • What is the NMR spectrum of Aspirin?
      • What are the safety handling issues for Thymol Blue?
  • 29. Complex Data and Information
  • 30. ChemSpider Searches
  • 31. ChemSpider Searches
  • 32. ChemSpider Complex Searches
  • 33. Question Everything online:
  • 34. Searching Dihydrogen Monoxide…
  • 35. Politicians, Chemistry and DHMO 
    • March 2004 , Aliso Viejo, California considered banning foam containers at city-sponsored events because dihydrogen monoxide is part of their production.
    • 2007 Jacqui Dean , New Zealand National Party MP write a letter to Associate Minister of Health Jim Anderton asking "Does the Expert Advisory Committee on Drugs have a view on the banning of this drug?"
  • 36. Caution! Question Everything!
  • 37. PubChem
  • 38. Vancomycin
    • Who will curate?
    • PubChem is not resourced to clean these errors
    • How would you clean such a large dataset?
  • 39. Vancomycin on ChemSpider 1 compound – discussions over 3 days
  • 40. The EXPERTS must get it right?!
  • 41. Wikipedia, C&E News, PubChem
    • C&E News (from ACS)
  • 42. Feedback from Steve Ritter
    • “ As for where we source our structures, our primary source is the researcher and peer-reviewed papers , because many compounds are novel.
    • ..we always double check them against one or more primary sources, typically Merck Index and SciFinder.
    • Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.”
  • 43. Feedback from Steve Ritter
    • “ As a rule, we at C&EN don’t use Wikipedia as a primary source for structures or chemical information, and I recommend that policy to anyone .”
    • “ It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day .”
  • 44. What About Digitonin?
  • 45. Comments on the Blog
    • Kirill Degtyarenko says:
    • September 15th, 2009 at 1:57 pm It looks like both ChEBI and Wikipedia structures are wrong as far as aglycon is concerned. According to
    • “… for the first time to confirm beyond all doubt the structure suggested by Tschesche and Wulff for digitonin by means of modern NMR techniques, and to assign all proton and carbon resonances.” Structure 1 shows methyl group at C-20 going UP, i.e. 20β (while by default spirostan is 20α).
  • 46. CAS as an authority
  • 47. The Blogging Community Participate
  • 48. Will it ever end?
    • The community says the structure of digitonin has “up” 20-Methyl.
    • If so, then multiple substances related to digitonin have OPPOSITE stereo at 20-Methyl
    • The spirostane skeleton has a “ down ” Methyl group so all spirostane-related structures would be wrong
  • 49. The FDA’s DailyMed
  • 50. Structures on DailyMed
  • 51. Lack of Stereochemisty
  • 52. Incorrect Structures
  • 53. Wow!
  • 54. Collaborative Knowledge Management
  • 55. Drugbank
  • 56. Taxol on PubChem
  • 57. The InChI Identifier
  • 58. Multiple Layers
  • 59. InChIStrings Hash to InChIKeys
  • 60. InChIs for Taxol
  • 61. Back to Taxol
    • Which one is correct???
  • 62. InChIKeys for Taxol
    • ChEBI and Wikipedia are the SAME structure
    • Drugbank is a DIFFERENT structure – ONE stereocenter
  • 63. Does one stereocenter matter?
  • 64. Does one stereocenter matter?
    • Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon
  • 65. Does one stereocenter matter?
    • Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, and Softenon
  • 66. Building a Structure Centric Community for Chemists
  • 67. Content is King and Quality Costs
    • Chemistry “content” is big money
      • Patent searching
      • Structures and properties
      • Drug databases
      • Literature databases
    • Chemical Abstracts Service (CAS), the “Gold Standard” in Chemistry related information
      • 101 years of content
      • $260 million revenue (2006)
      • >50 million substances
      • >60 million sequences
  • 68. ChemSpider Searches
  • 69. ChemSpider Searches
  • 70. InChIKey Searches Work
  • 71. The InChI “Resolver”
  • 72. Assertion and Chemical Entities
    • Who says what Taxol is?
    • What is the “timeline” for a molecule?
    • How do we clean up the Public data?
  • 73. Crowdsourcing
  • 74. Depositions From Crowds
    • CAS indexes published literature, patents and chemical vendors ( indexes ChemSpider too )
    • “ Lost Chemistry”
      • syntheses in theses
      • lab notebooks
      • compounds in private collections
    • ChemSpider accepts public depositions: structures, text, spectra, images.
  • 75. Crowd-sourcing Chemistry Curation
    • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
  • 76. “ Lathosterol”
  • 77. “ Lathosterol”
  • 78. “ Lathosterol”
  • 79. “ Lathosterol” Removed
  • 80.  
  • 81. “ Lathosterol” on PubChem
  • 82. “ Lathosterol” on PubChem
  • 83. “ Lathosterol” on PubChem
  • 84. Validate Names for PubMed “Caldarchaeol”
  • 85. Publishers are experimenting
    • … invited researchers to prototype tools dealing with the ever-increasing amount of online life sciences information
    • The winners built:
    • Reflect: Automated Annotation of Scientific Terms :
  • 86. Reflect
  • 87. Entity-Extraction, Mark-up, Annotate
  • 88. Success Depends on Dictionaries
  • 89. Structure Searching Articles…
    • Searching articles based on chemical structure and substructure is very expensive.. but is changing
    • The web IS ready - when will publishers deliver?
      • Structures can be shown
      • Spectra can be interactive
      • Graphics don’t need to be static
      • Publishers can enhance their articles
  • 90. Semantic Mark-up for Chemistry
    • Semantic mark-up for chemistry is here
      • RSC project prospect (structure linking, IUPAC Gold Book ontology and other ontologies
      • Nature publishing group compound linking
      • ChemSpider Journal of Chemistry
  • 91. Nature Chemistry Compound Pages
  • 92. ChemSpider and Publishing
    • Curation led to a set of validated dictionaries
    • Integrated best-in-class entity extraction with validated name dictionaries
    • Additional dictionaries gave reactions, groups, families, hardware and software vendors etc
  • 93. ChemMantis and CJOC
  • 94. Name-Structure Pairs
  • 95. Converting Detected Names…
    • Names are searched against a validated dictionary (this expands as ChemSpider is curated)
    • If not found then they are passed through a Name to Structure algorithm
    • If they cannot convert then ChemSpider is searched for non-validated names
  • 96. Deposit Structures
  • 97. Custom Dictionaries
    • Entity Extraction built around modified algorithms from SureChem
    • Optimized for “publications”
    • Dictionaries for chemical entities, groups, reactions, elements, families, species…
    • Dictionaries can be expanded
  • 98. Species – linked to Wikipedia
  • 99. Semantic Linking of Structures
    • What would you want to link off a structure?
      • Chemical suppliers
      • Other publications
      • Analytical Data
      • Related Reactions
      • Wikipedia
      • Patents
      • “ Everything”
  • 100. RSC’s Project Prospect
  • 101. In Development ChemSpider Synthesis
    • ChemSpider Synthesis will be a home for all things “synthetic”
    • An online resource for synthetic procedures from blogs, other online resources, RSC supplementary info, other publishers etc.
    • Public peer-review and feedback for synthetic procedures
  • 102. RSC Supplementary Info
  • 103. RSC Supplementary Info
  • 104. Online Journals and Live Data
  • 105. ChemSpider Everywhere : Embed
  • 106. ChemSpider Everywhere: Spectral Game
  • 107. ChemSpider Everywhere Crowdsourced Curation of Spectra Building a Structure Centric Community for Chemists
  • 108. ChemSpider Everywhere ChemMobi Building a Structure Centric Community for Chemists
  • 109. ChemSpider Everywhere
    • Linked from Wikipedia
    • Linked from Open Notebook Science sites
    • Linked from Blogs using Structure/Spectra EMBED
    • Integrated into structure drawing packages such as ACD/ChemSketch, Symyx Draw, Open Source applets
    • Integrated to software offerings from Thermo, Waters, Agilent, Bruker
  • 110.  
  • 111. It’s a long road ahead…
  • 112. More representative…
  • 113. Where is ChemSpider Lacking?
    • ChemSpider is limited to “defined chemicals”. No support for:
      • Polymers
      • Minerals
      • Markush structures
    • ChemSpider is very dependent on InChIs
      • Stereochemistry around non-carbon centers
      • Organometallics are not correctly represented
    • There are millions of errors on ChemSpider
  • 114. What’s next?
    • Keep cleaning and depositing data
    • Deprecate/redeposit at PubChem
    • Layer on RDF for the semantic web
    • Integrate software: Symyx Jdraw, NMRShiftDB
    • Integrate RSC content – a massive archive!
    • Integrate RSC publishing workflows and databases
  • 115. You are invited..
    • Curate ChemSpider data and link to us
    • Deposit your data with us
      • Structures
      • Spectra
      • Synthesis procedures
    • ChemSpider Synthesis is under development
    • Help assert what is Digitonin?
  • 116. How Was ChemSpider Built?
    • ChemSpider was a “hobby project”
    • Housed in a basement and running off three servers – one bought, two built
    • Sensitive to weather and power stability
    • Went live at ACS Spring 2007 in Chicago
  • 117. Not in a basement now...
  • 118. And the Downside
  • 119. Thank you [email_address] Twitter: ChemSpiderman SLIDES: