Your SlideShare is downloading. ×
0
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data?

2,604

Published on

This presentation was given at the Wolfram Data Summit in Washington DC on Sept 9th 2010 as part of a panel series of presentations and discussions on crowdsourcing approaches for data. It was a rant …

This presentation was given at the Wolfram Data Summit in Washington DC on Sept 9th 2010 as part of a panel series of presentations and discussions on crowdsourcing approaches for data. It was a rant by me on the quality of what's online and questioning "who cares".

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
2,604
On Slideshare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
12
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. Crowdsourced Curation of Chemistry Data. How Bad is Online Chemistry Data? Antony Williams Wolfram Summit, September 2010
  • 2. 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/correct data
  • 3. www.chemspider.com
  • 4. We Answer 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?
  • 5. Search for a Chemical…by name
  • 6. Available Information…
    • Linked to vendors, safety data, toxicity, metabolism
  • 7. Available Information….
  • 8. Search for chemicals
  • 9. ChemSpider Today
    • 24.8 million structures
    • 400 data sources
    • Grows daily
    • Community annotation and curation
    • We curate, edit, change, enhance data daily
  • 10. Linked Data on the Web
  • 11. Three Years of Experience
    • Internet-based chemistry is a mess !
    • Most public compound databases on the web are contaminated . Including ours !
    • 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 ?
  • 12. 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
  • 13. What is the Structure of Vitamin K?
  • 14. MeSH – Medical Subject Headings
    • 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
  • 15. What is the Structure of Vitamin K1?
  • 16. What is the Structure of Vitamin K1?
  • 17. Chemical Abstracts “Common Chemistry” Database
  • 18. Wikipedia
  • 19.  
  • 20. Incorrect Structures
  • 21. Wow!
  • 22. Lack of Stereochemistry
  • 23. Does stereochemistry matter?
    • Distaval, Talimol, Nibrol, Sedimide, Quietoplex, Contergan, Neurosedyn, Softenon, Thalidomide
  • 24.  
  • 25.  
  • 26.  
  • 27. PubChem
  • 28.  
  • 29.
    • “ 2-methyl-3-(3,7,11,15-tetramethyl hexadec-2-enyl)naphthalene-1,4-dione”
    • Variants of systematic names on PubChem
    • 2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl
    • 2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl
    • 2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl
    • 2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl
    • 2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl
    • 2-methyl-3-[(E)-3,7,11,15-tetramethyl
    • 2-methyl-3-(3,7,11,15-tetramethyl
    • 2-methyl-3-[(E)-3,7,11,15-tetramethyl
  • 30. ChEBI – Manual Curation
  • 31.  
  • 32.  
  • 33.  
  • 34. What’s Methane?
  • 35. What’s Methane?
  • 36. What ELSE is Methane???
  • 37. The EXPERTS must get it right?!
  • 38. Wikipedia, C&E News, PubChem
    • C&E News (from ACS)
  • 39. 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
  • 40. Search “Vitamin H”
  • 41. Search “Vitamin H”
  • 42. “ Curate” Identifiers
  • 43. “ Curate” Identifiers
  • 44. “ Curate” Identifiers
  • 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. Crowdsourced “Annotations”
    • Registered Users can add
      • Descriptions/Syntheses/Commentaries
      • Links to articles, blogs, wikis etc
      • Add spectral data
      • Add photos
      • Add MP3 files
      • Add Videos
  • 47. Data Validation – Not Vitamin K1
  • 48. Data Validation – Not Beclamethasone Dipropionate DailyMed Article
  • 49. Data Validation …NOT Cholesterol
  • 50. Data Validation – ONE Cymarin Question Quality in Big Databases
  • 51. First request to Database Hosts!
    • Every public compound database host should add ONE feature – “Leave Comments”
  • 52. Second request to Database Hosts! Show Comments
  • 53. Always Question Online Chemistry
  • 54. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

×