Delivering Curated Chemistry to the World via Crowdsourced Deposition and Annotation on ChemSpider


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RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to chemists. We will discuss some of the challenges associated with validating data quality and examine how ChemSpider is a part of the new “semantic web for chemistry”. ChemSpider has also spawned a number of additional projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles, Learn Chemistry Wiki for students learning chemistry and SpectraSchool for learning spectroscopy.

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Delivering Curated Chemistry to the World via Crowdsourced Deposition and Annotation on ChemSpider

  1. 1. Delivering Curated Chemistry to the World via Crowdsourced Deposition and Annotation on ChemSpider Antony Williams University of Chicago, January 27 th 2012
  2. 2. The World of Online Chemistry <ul><li>Property databases </li></ul><ul><li>Compound aggregators </li></ul><ul><li>Screening assay results </li></ul><ul><li>Scientific publications </li></ul><ul><li>Encyclopedic articles (Wikipedia) </li></ul><ul><li>Metabolic pathway databases </li></ul><ul><li>ADME/Tox data – eTOX for example </li></ul><ul><li>Blogs/Wikis and Open Notebook Science </li></ul><ul><li>Contributing Open Source code to projects </li></ul>
  3. 3. We Have …Too Much Data!!!
  4. 4. e-Science and Primary Data <ul><li>How much data generated in a lab, that COULD go public, is lost forever? </li></ul>
  5. 5.
  6. 6. e-Science and Primary Data <ul><li>How much data generated in a lab, that COULD go public, is lost forever? </li></ul><ul><li>Public Domain reference databases of value? </li></ul><ul><ul><li>Syntheses </li></ul></ul><ul><ul><li>Properties </li></ul></ul><ul><ul><li>Spectra </li></ul></ul><ul><ul><li>CIFs </li></ul></ul><ul><ul><li>Images </li></ul></ul>
  7. 7. PubChem
  8. 8. ChEMBL
  9. 9. Collaborative Knowledge Management
  10. 10. e-Science and Primary Data <ul><li>How much data generated in a lab, that COULD go public, is lost forever? </li></ul><ul><li>Public Domain reference databases of value? </li></ul><ul><ul><li>Syntheses </li></ul></ul><ul><ul><li>Properties </li></ul></ul><ul><ul><li>Spectra </li></ul></ul><ul><ul><li>CIFs </li></ul></ul><ul><ul><li>Images </li></ul></ul><ul><li>Much of chemistry is chemical structure-based – where and how could we host these data? </li></ul>
  11. 11. RSC’s ChemSpider
  12. 12. Available Information… <ul><li>Linked to vendors, safety data, toxicity, metabolism </li></ul>
  13. 13. Available Information….
  14. 14. Crowdsourced “Annotations” <ul><li>Users can add </li></ul><ul><ul><li>Descriptions/Syntheses/Commentaries </li></ul></ul><ul><ul><li>Links to PubMed articles </li></ul></ul><ul><ul><li>Links to articles via DOIs </li></ul></ul><ul><ul><li>Add spectral data </li></ul></ul><ul><ul><li>Add Crystallographic Information Files </li></ul></ul><ul><ul><li>Add photos </li></ul></ul><ul><ul><li>Add MP3 files </li></ul></ul><ul><ul><li>Add Videos </li></ul></ul>
  15. 16. Spectra
  16. 17. Spectra
  17. 18. Data on the Web
  18. 19. Chemistry Data online is messy <ul><li>We have inherited errors </li></ul><ul><li>All public compound databases, including ours, have errors </li></ul><ul><li>“ Incorrect” structures – assertions, timelines etc </li></ul><ul><li>“ Incorrect” names associated with structures </li></ul><ul><li>Properties </li></ul><ul><li>Links </li></ul><ul><li>Publications </li></ul><ul><li>ENORMOUS CHALLENGE </li></ul>
  19. 20. The Structure of Vitamin K?
  20. 21. MeSH <ul><li>A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants , VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K </li></ul>
  21. 22. The Structure of Vitamin K1?
  22. 23. What is the Structure of Vitamin K1?
  23. 24. CAS’s Common Chemistry
  24. 25. Wikipedia
  25. 28. ChEBI – Manual Curation
  26. 32. <ul><li>“ 2-methyl-3-(3,7,11,15-tetramethyl hexadec-2-enyl)naphthalene-1,4-dione” </li></ul><ul><li>Variants of systematic names on PubChem </li></ul><ul><li>2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-[(E)-3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-(3,7,11,15-tetramethyl </li></ul><ul><li>2-methyl-3-[(E)-3,7,11,15-tetramethyl </li></ul>
  27. 33. Question Everything online:
  28. 34. It’s all on Wikipedia…
  29. 35. Chemistry on The Internet Is Messy
  30. 36. It’s Methane…
  31. 37. What’s Methane?
  32. 38. What’s Methane?
  33. 39. What ELSE is Methane???
  34. 41. EPA’s DailyMed
  35. 42. EPA’s DailyMed
  36. 43. EPA’s DailyMed
  37. 44. PHYSPROP Database <ul><li>The freely downloadable database under the EPI Suite prediction software </li></ul><ul><li>Very Basic filters suggest data quality issues </li></ul>
  38. 45. The Stereochemistry challenge. 12500 chemicals with “missed” stereo
  39. 46. With Great Fanfare…
  40. 47. NPC Browser
  41. 48. NPC Browser
  42. 50. Openness and Quality Issues Williams and Ekins, DDT, 16: 747-750 (2011) Science Translational Medicine 2011
  43. 51. Public Domain Databases <ul><li>Our databases are a mess… </li></ul><ul><li>Non-curated databases are proliferating errors </li></ul><ul><li>We source and deposit data between databases </li></ul><ul><li>Original sources of errors hard to determine </li></ul><ul><li>Curation is time-consuming and challenging </li></ul>
  44. 52. Stop Whining – Fix it
  45. 53. Crowdsourced Curation <ul><li>Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate </li></ul>
  46. 54. Search “Vitamin H”
  47. 55. “ Curate” Identifiers
  48. 56. “ Curate” Identifiers
  49. 57. “ Curate” Identifiers
  50. 58. Standards : Structure Standardization
  51. 59. Standards : Structure Standardization
  52. 60. Standards : Structure Standardization
  53. 61. What needs to happen? <ul><li>Standards </li></ul><ul><ul><li>Standardization of structures </li></ul></ul><ul><ul><ul><li>ChEBI/PubChem sharing </li></ul></ul></ul><ul><ul><ul><li>InChI adoption </li></ul></ul></ul>
  54. 62. The InChI Identifier
  55. 63. Multiple Layers
  56. 64. InChIStrings Hash to InChIKeys
  57. 65. Vancomycin – Search the Internet
  58. 66. Vancomycin Search Molecular SKELETON Search Full Molecule
  59. 67. Full Skeleton Search: 104 Hits
  60. 68. Full Molecule Search: 4 Hits
  61. 69. Crowdsourcing Works <ul><li>>130 people have deposited data and participated in data curation </li></ul><ul><li>Different level curators check each other </li></ul><ul><li>More curators and depositors are encouraged! </li></ul>
  62. 70. What needs to happen? <ul><li>Standards </li></ul><ul><ul><li>Standardization of structures </li></ul></ul><ul><ul><ul><li>ChEBI/PubChem sharing </li></ul></ul></ul><ul><ul><ul><li>InChI adoption </li></ul></ul></ul><ul><li>Collaboration </li></ul><ul><ul><li>Stop reinventing the wheel </li></ul></ul><ul><ul><li>Share data, share efforts and speed the process </li></ul></ul>
  63. 71. Antony Williams vs Identifiers Passport ID Dad, Tony, others SSN Green Card License 5 email addresses ChemSpiderman (blog, Twitter account, Facebook, Friendfeed) OpenID … .
  64. 72. Aspirin names and synonyms <ul><li>Text searches depend on correct association </li></ul><ul><li>335 suggested identifiers for Aspirin just on PubChem! </li></ul><ul><li>Disambiguation dictionaries are necessary, not just for authors! </li></ul>
  65. 75. The Final Search Strategy
  66. 76. All Those Names, One Structure
  67. 77. Ambiguity in Identifiers
  68. 78. Curated Dictionaries Matter
  69. 79. Success Depends on Dictionaries
  70. 80. Validated Name-Structure Dictionaries <ul><li>Chemical name dictionaries are used for: </li></ul><ul><ul><ul><li>Text-mining (publications, patents) </li></ul></ul></ul><ul><ul><ul><ul><li>Used to index PubMed and link to Google Patents </li></ul></ul></ul></ul><ul><ul><ul><li>Linking to other databases – think Biology! </li></ul></ul></ul><ul><ul><ul><ul><li>When structures are not available drug names link </li></ul></ul></ul></ul><ul><ul><ul><li>Searching the web </li></ul></ul></ul><ul><ul><ul><ul><li>Names link to structures link to InChIs </li></ul></ul></ul></ul>
  71. 81. I want to know about “Vincristine” If all algorithms work then everything on the page is correct by default except the name-structure relationship!
  72. 82. Vincristine: Identifiers and Properties
  73. 83. Vincristine: Vendors and Sources Linked by Structure
  74. 84. Vincristine: Patents Linked by Name
  75. 85. Vincristine: Articles Linked by Name
  76. 86. Challenges of Complex Molecules Yohimbine
  77. 87. Originally 15 compounds “called” Yohimbine 54 Skeletons for Yohimbine
  78. 88. <ul><ul><li>Internal and external content </li></ul></ul><ul><ul><li>Built to meet primary use-case </li></ul></ul><ul><ul><li>Tailored indexes and GUIs </li></ul></ul><ul><ul><li>Internal unique language & metadata </li></ul></ul><ul><ul><li>Poor interoperability/integration </li></ul></ul><ul><ul><li>Powerpoint, Documents, Excel </li></ul></ul><ul><ul><li>Many suppliers of systems and content in a single workflow </li></ul></ul>Pharma Information Tombs Literature Patents News Pipeline SAR CSRs Safety In vivo Etc
  79. 89. What could create change? <ul><li>Harvard Business Review (2010) </li></ul><ul><li>“ One change would make a substantial difference [ to drug R&D ] : the creation of agreed-upon standards for digitally representing drug assets. ” </li></ul>
  80. 90. It is so difficult to navigate… What’s the structure? Are they in our file? What’s similar? What’s the target? Pharmacology data? Known Pathways? Working On Now? Connections to disease? Expressed in right cell type? Competitors? IP?
  81. 91. <ul><li>Open PHACTS Project </li></ul><ul><li>Develop a set of robust standards… </li></ul><ul><li>Implement the standards in a semantic integration hub </li></ul><ul><li>Deliver services to support drug discovery programs in pharma and public domain </li></ul><ul><li>22 partners, 8 pharmaceutical companies, 3 biotechs </li></ul><ul><li>36 months project </li></ul>Guiding principle is open access, open usage, open source - Key to standards adoption -
  82. 93. ChemSpider Resources for Chemistry
  83. 94. 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 Internet Data
  84. 95. The Future of Chemistry on the Web? <ul><li>Public compound databases federate & build a linked environment of validated data! </li></ul><ul><li>Data validation needs are not ignored </li></ul><ul><li>Publishers layer on information to make publications discoverable </li></ul><ul><li>Public-Private databases can be linked </li></ul><ul><li>Open Data proliferate </li></ul><ul><li>The “ Semantic Web ” in action </li></ul>
  85. 96. Acknowledgments <ul><li>The ChemSpider team </li></ul><ul><li>Our data providers, depositors, collaborators and curators </li></ul><ul><li>Software providers – OpenEye, ChemDoodle, ACD/Labs, GGA Software, Open Source (Jmol, JSpecView, OpenBabel) </li></ul><ul><li>Sean Ekins @collabchem </li></ul>
  86. 97. Thank you Email: Twitter: ChemConnector Blog: Personal Blog: SLIDES: