ChemSpider as a Platform for Crowd Participation in Curating Chemistry

  • 1,225 views
Uploaded on

This is a presentation I gave at the International Digital Curation Conference in Chicago, December 7th 2010, #idcc10. The presentation discusses the issues of data quality and the need for …

This is a presentation I gave at the International Digital Curation Conference in Chicago, December 7th 2010, #idcc10. The presentation discusses the issues of data quality and the need for collective, crowdsourced efforts to improve the quality of chemistry related data on the Internet

More in: Technology
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
1,225
On Slideshare
0
From Embeds
0
Number of Embeds
0

Actions

Shares
Downloads
7
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. ChemSpider as a Platform for Crowd Participation in Curating Chemistry Antony Williams IDCC, Chicago, December 2010
  • 2. WARNING: Chemistry is Dangerous
  • 3. Di-Hydrogen Monoxide
  • 4. Di-Hydrogen Monoxide
    • 2H
  • 5. Di-Hydrogen Monoxide
    • 2H + 1O
  • 6. Di-Hydrogen Monoxide
    • H2O
  • 7. Di-Hydrogen Monoxide
    • H2O
    • Water
  • 8. It’s all on Wikipedia…
  • 9. Chemistry on the Internet – Not All Bad
    • 100s of websites hosting chemistry-related data
    • Chemistry information is generally “compound-based”
      • Chemical “structures”
      • Identifiers, names and synonyms
      • Properties
      • Analytical data
      • How to synthesize
      • Articles, patents, safety information
    • Chemistry “language and dialects”
  • 10. Dialects describing chemicals
  • 11. A Pragmatic Vision
      • “ Build a Structure Centric Community”
    • Integrate chemistry across the internet based on “chemical structure”
      • A “structure-based hub” to information and data
      • Let chemists contribute their own data
      • Allow the community to curate & annotate data
  • 12. www.chemspider.com
  • 13. Answering Questions for Chemists
    • Questions a chemist might ask…
      • What is the melting point of n-heptanol?
      • 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 Aspirin?
      • What is the NMR spectrum of Benzoic Acid?
      • What are the safety handling issues for toluene?
  • 14. Search for a Chemical…by name
  • 15. Available Information…
    • Linked to chemical vendors, safety data, toxicity, metabolism…
  • 16. Available Information….
  • 17. ChemSpider Today
    • Almost 25 million unique chemicals
    • Over 400 data sources
    • Grows daily – community and RSC depositions
    • Community annotation and curation
    • We curate, edit, change, enhance data daily
  • 18. Three Years of Experience
    • Internet-based chemistry is a mess !
    • Public compound databases are contaminated
    • The annotation/curation of data online is difficult
    • Most database hosts are non-responsive to feedback – “We are a host/repository of data”
    • Who cares ?
  • 19. Linked Data on the Web
  • 20. Where is chemistry online?
    • Encyclopedic articles (Wikipedia)
    • Chemical vendor databases
    • Metabolic pathway databases
    • Property databases
    • Patents with chemical structures
    • Drug Discovery data
    • Scientific publications
    • Compound aggregators
    • Blogs/Wikis and Open Notebook Science
  • 21. What is the Structure of Vitamin K?
  • 22. MeSH – Medical Subject Headings
    • 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).
  • 23. What is the Structure of Vitamin K1?
  • 24. What is the Structure of Vitamin K1?
  • 25. Chemical Abstracts “Common Chemistry” Database
  • 26. Wikipedia
  • 27.  
  • 28. Incorrect Structures
  • 29. Lack of Stereochemistry
  • 30. Does stereochemistry matter?
    • Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
  • 31.  
  • 32. PubChem
  • 33.  
  • 34.  
  • 35. What’s Methane?
  • 36. What’s Methane?
  • 37. What ELSE is Methane???
  • 38. Internet-Based Chemistry is a Mess
    • Algorithms can get you so far
    • Human curation is necessary
    • Only the crowds can help with big data… ChemSpider is approaching 25 million compounds
  • 39. Search “Vitamin H”
  • 40. Search “Vitamin H”
  • 41. “ Curate” Identifiers
  • 42. “ Curate” Identifiers
  • 43. “ Curate” Identifiers
  • 44. Crowd-sourcing Chemistry Curation
    • Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
  • 45. “ Curate” Identifiers
    • General curation activities
      • Remove incorrect names
      • Correct spellings
      • Add multilingual names
      • Add alternative names
    • In 3 years over 1 million structure-identifier relationships have been validated – robotically and manually
    • 130 people have participated in validation or annotation. “ Crowds ” can be quite small!
  • 46. Crowdsourcing Works
    • The “crowd” has deposited data (structures, spectra, etc) and participated in data curation
    • Different level curators check each others work
    • Wikipedia is the modern primary example
    • Some curators are “madmen”…
  • 47. Crowdsourcing Works
    • The “crowd” has deposited data (structures, spectra, etc) and participated in data curation
    • Different level curators check each others work
    • Wikipedia is the modern primary example
    • Some curators are “madmen”…
    • The Oxford English Dictionary
  • 48. Vancomycin – Curate This!!!
  • 49. Vancomycin on ChemSpider 1 compound – 3 days
  • 50. Crowdsourced “Annotations”
    • Users can add
      • Descriptions/Syntheses/Commentaries
      • Links to articles
      • Spectral data
      • Photos
      • MP3 files
      • Videos
  • 51. Multimedia Content Holder
  • 52. Gaming for Curation of Spectra
  • 53. ChemSpider Everywhere Crowdsourced Curation of Spectra
  • 54. Data Curation
  • 55. True Curation of Data
  • 56. ChemSpider SyntheticPages
  • 57. Drug Name Generic Name ChEBI ChemSpider CAS Com. Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia Spiriva Tiotropium Bromide No Hits  No Hits    4/0  Depakote Valproate semisodium        No Structure Basen Voglibose   No Hits  No Hits  2/1  Symbicort 1) Budesonide       8/1  Symbicort 2) Formoterol WRONG  No Hits    6/1  Vytorin 1) Ezetimibe   No Hits      Vytorin 2) Simvastatin       2/1  Taxol Paclitaxel       44/1  Thalidomid Thalidomide No Hits        Zocor Simvastatin       2/1  Crestor Rosuvastatin   No Hits    2/1 
  • 58. Sharing Our Activities
    • Presently defining approaches with other public compound databases to share results of curation activities
    • Member of large European project to link data from the Life Sciences. Sharing results of curation is essential
    • Making curation and contribution interfaces Mobile
  • 59. Mobile ChemSpider
  • 60. First request to Database Hosts!
    • Every public compound database host should add ONE feature – “Leave Comments”
  • 61. Second request to Database Hosts! Show Comments
  • 62. Question Quality
  • 63. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams