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Navigating an Internet of  Chemistry via ChemSpider Antony Williams University of Arkansas, Little Rock, October 2011 UALR...
Overview <ul><li>What type of chemistry is available on the internet? </li></ul><ul><li>Representative flavors of chemistr...
Where is chemistry online? <ul><li>Encyclopedic articles (Wikipedia) </li></ul><ul><li>Chemical vendor databases </li></ul...
Representative Flavors of Chemistry
Molfiles <ul><li>Molfiles are the primary exchange format between structure drawing packages </li></ul><ul><li>Can be diff...
Molfiles <ul><li>10  9  0  0  1  0  0  0  0  0  1 V2000 </li></ul><ul><li>31.2937  -9.0366  0.0000 C  0  0  0  0  0  0  0 ...
SMILES ( http://en.wikipedia.org/wiki/SMILES ) <ul><li>SMILES is a common format  </li></ul><ul><li>Can support polymers, ...
Stereo
Tautomeric forms
Vendor-dependent SMILES <ul><li>ACD/Labs </li></ul><ul><li>CC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(C)=CCC2=C(C)C(=O)c1ccccc1C2=O...
The InChI Identifier
InChI <ul><li>SINGLE code base managed by IUPAC – integrated into drawing packages. No variability as with SMILES </li></u...
Multiple Layers
Tautomers – “Mobile H Perception”
Stereo
Checking for Stereochemistry
Checking for Stereochemistry Use your drawing package!
Checking for Stereochemistry
Checking for Stereochemistry
Checking for Stereochemistry
Databases and Standardization
Databases and Standardization
InChIStrings Hash to InChIKeys
Vancomycin
Vancomycin Search Molecular SKELETON Search Full Molecule
Searching Chemistry on the Internet <ul><li>Searching Vincristine </li></ul><ul><ul><li>Name searching Google </li></ul></...
Searching Chemistry on the Internet <ul><li>Searching Vincristine </li></ul><ul><ul><li>Name searching Google </li></ul></...
www.chemspider.com
I want to know about “Vincristine”
Vincristine: Identifiers and Properties
Vincristine: Identifiers and Properties
Vincristine: Vendors and Sources
Vincristine: Patents
Vincristine: Articles
Vancomycin Search Molecular SKELETON Search Full Molecule
Full  Skeleton  Search: 104 Hits
Full  Molecule  Search: 4 Hits
Quality on the Internet <ul><li>Trust everything on the web??? </li></ul>
What’s said on the web is true…
What’s said on the web is true…
What’s said on the web is true… <ul><li>“ We then established a collaboration with professor Sum Ting Wong, a fugitive fro...
Contributing Chemistry to the Web <ul><li>If it was not just about me </li></ul>
Contributing Chemistry to the Web <ul><li>If it was not just about me </li></ul><ul><li>We might have a community built en...
Contributing Chemistry to the Web <ul><li>If it was not just about me </li></ul><ul><li>We might have a community built en...
Contributing Chemistry to the Web <ul><li>ChemSpider as a host for community contributions </li></ul><ul><ul><li>Curation ...
Contributing Chemistry to the Web <ul><li>Sites allow direct feedback – leave it! </li></ul><ul><li>Sites allow deposition...
Spectra
ChemSpider SyntheticPages
Submission Process <ul><li>Simple template-based submission process </li></ul><ul><li>Submissions reviewed by editorial bo...
Conclusion <ul><li>Diverse types of chemistry are available on the web </li></ul><ul><li>Searching of the internet is poss...
Thank you Email: williamsa@rsc.org  Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector....
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Navigating an Internet of Chemistry via ChemSpider

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This is a presentation I gave via the BigBlueButton system to students and faculty at the University of Arkansas, Little Rock, regarding searching the internet for Chemistry.

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Navigating an Internet of Chemistry via ChemSpider

  1. 1. Navigating an Internet of Chemistry via ChemSpider Antony Williams University of Arkansas, Little Rock, October 2011 UALR Chemistry Seminar Guest Lecture
  2. 2. Overview <ul><li>What type of chemistry is available on the internet? </li></ul><ul><li>Representative flavors of chemistry </li></ul><ul><li>How can the internet be searched by chemical? </li></ul><ul><li>Quality on the Internet </li></ul><ul><li>Contributing to the chemistry internet </li></ul>
  3. 3. Where is chemistry online? <ul><li>Encyclopedic articles (Wikipedia) </li></ul><ul><li>Chemical vendor databases </li></ul><ul><li>Metabolic pathway databases </li></ul><ul><li>Property databases </li></ul><ul><li>Patents with chemical structures </li></ul><ul><li>Drug Discovery data </li></ul><ul><li>Scientific publications </li></ul><ul><li>Compound aggregators </li></ul><ul><li>Blogs/Wikis and Open Notebook Science </li></ul>
  4. 4. Representative Flavors of Chemistry
  5. 5. Molfiles <ul><li>Molfiles are the primary exchange format between structure drawing packages </li></ul><ul><li>Can be different between different drawing packages </li></ul><ul><li>Most commonly carry X,Y coordinates for layout </li></ul><ul><li>Can support polymers, organometallics, etc. </li></ul><ul><li>Can carry 3D coordinates </li></ul>
  6. 6. Molfiles <ul><li>10 9 0 0 1 0 0 0 0 0 1 V2000 </li></ul><ul><li>31.2937 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>26.6526 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>31.2937 -7.7066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>30.1161 -9.6877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>25.5096 -9.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>28.9731 -9.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>27.8163 -9.7016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>26.6664 -7.7066 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>32.4367 -9.6877 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>30.1161 -11.0177 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 </li></ul><ul><li>3 1 2 0 0 0 0 </li></ul><ul><li>4 1 1 0 0 0 0 </li></ul><ul><li>9 1 1 0 0 0 0 </li></ul><ul><li>7 2 1 0 0 0 0 </li></ul><ul><li>5 2 2 0 0 0 0 </li></ul><ul><li>8 2 1 0 0 0 0 </li></ul><ul><li>6 4 1 0 0 0 0 </li></ul><ul><li>4 10 1 6 0 0 0 </li></ul><ul><li>7 6 1 0 0 0 0 </li></ul><ul><li>M END </li></ul>
  7. 7. SMILES ( http://en.wikipedia.org/wiki/SMILES ) <ul><li>SMILES is a common format </li></ul><ul><li>Can support polymers, organometallics, etc. </li></ul><ul><li>Does NOT carry X,Y or Z coordinates for layout so requires layout algorithms – can be problematic! </li></ul><ul><li>Generally different between drawing packages </li></ul>
  8. 8. Stereo
  9. 9. Tautomeric forms
  10. 10. Vendor-dependent SMILES <ul><li>ACD/Labs </li></ul><ul><li>CC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(C)=CCC2=C(C)C(=O)c1ccccc1C2=O </li></ul><ul><li>OpenEye </li></ul><ul><li>CC1=C(C(=O)c2ccccc2C1=O)C/C=C(C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C </li></ul><ul><li>ChEMBL </li></ul><ul><li>CC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(=CCC1=C(C)C(=O)c2ccccc2C1=O)C </li></ul>
  11. 11. The InChI Identifier
  12. 12. InChI <ul><li>SINGLE code base managed by IUPAC – integrated into drawing packages. No variability as with SMILES </li></ul><ul><li>InChI Strings can be reversed to structures – same problem as with SMILES – no layout </li></ul><ul><li>Adopted by the community (databases, blogs, Wikipedia) – good for searching the internet </li></ul>
  13. 13. Multiple Layers
  14. 14. Tautomers – “Mobile H Perception”
  15. 15. Stereo
  16. 16. Checking for Stereochemistry
  17. 17. Checking for Stereochemistry Use your drawing package!
  18. 18. Checking for Stereochemistry
  19. 19. Checking for Stereochemistry
  20. 20. Checking for Stereochemistry
  21. 21. Databases and Standardization
  22. 22. Databases and Standardization
  23. 23. InChIStrings Hash to InChIKeys
  24. 24. Vancomycin
  25. 25. Vancomycin Search Molecular SKELETON Search Full Molecule
  26. 26. Searching Chemistry on the Internet <ul><li>Searching Vincristine </li></ul><ul><ul><li>Name searching Google </li></ul></ul><ul><ul><li>Name searching Wikipedia </li></ul></ul><ul><ul><li>Name searching Wolfram Alpha </li></ul></ul><ul><ul><li>Name, name, name, name…searching </li></ul></ul><ul><ul><li>Structure searching DOZENS of websites, each with different information or… </li></ul></ul>
  27. 27. Searching Chemistry on the Internet <ul><li>Searching Vincristine </li></ul><ul><ul><li>Name searching Google </li></ul></ul><ul><ul><li>Name searching Wikipedia </li></ul></ul><ul><ul><li>Name searching Wolfram Alpha </li></ul></ul><ul><ul><li>Name, name, name, name…searching </li></ul></ul><ul><ul><li>Structure searching DOZENS of websites, each with different information or… </li></ul></ul><ul><ul><li>Search ONE website integrating the others! </li></ul></ul>
  28. 28. www.chemspider.com
  29. 29. I want to know about “Vincristine”
  30. 30. Vincristine: Identifiers and Properties
  31. 31. Vincristine: Identifiers and Properties
  32. 32. Vincristine: Vendors and Sources
  33. 33. Vincristine: Patents
  34. 34. Vincristine: Articles
  35. 35. Vancomycin Search Molecular SKELETON Search Full Molecule
  36. 36. Full Skeleton Search: 104 Hits
  37. 37. Full Molecule Search: 4 Hits
  38. 38. Quality on the Internet <ul><li>Trust everything on the web??? </li></ul>
  39. 39. What’s said on the web is true…
  40. 40. What’s said on the web is true…
  41. 41. What’s said on the web is true… <ul><li>“ We then established a collaboration with professor Sum Ting Wong, a fugitive from the North Korean University Hu Yu Hai Ding, currently in Rome (Italy).” </li></ul><ul><li>“ This was identified as the new protein Wai So Dim (WSD).” </li></ul>
  42. 42. Contributing Chemistry to the Web <ul><li>If it was not just about me </li></ul>
  43. 43. Contributing Chemistry to the Web <ul><li>If it was not just about me </li></ul><ul><li>We might have a community built encyclopedia </li></ul><ul><li>I might know where the best restaurants are </li></ul><ul><li>I might get good advice on books to read </li></ul><ul><li>I might know which movies to watch </li></ul><ul><li>I might know which plumber to call </li></ul><ul><li>Data might just be Open </li></ul>
  44. 44. Contributing Chemistry to the Web <ul><li>If it was not just about me </li></ul><ul><li>We might have a community built encyclopedia </li></ul><ul><li>I might know where the best restaurants are </li></ul><ul><li>I might get good advice on books to read </li></ul><ul><li>I might know which movies to watch </li></ul><ul><li>I might know which plumber to call </li></ul><ul><li>Data might just be Open </li></ul>
  45. 45. Contributing Chemistry to the Web <ul><li>ChemSpider as a host for community contributions </li></ul><ul><ul><li>Curation and validation input </li></ul></ul><ul><ul><li>Structures </li></ul></ul><ul><ul><li>Movies </li></ul></ul><ul><ul><li>Images </li></ul></ul><ul><ul><li>Analytical data – especially spectra </li></ul></ul>
  46. 46. Contributing Chemistry to the Web <ul><li>Sites allow direct feedback – leave it! </li></ul><ul><li>Sites allow deposition of data </li></ul><ul><ul><li>Text – chemical names, properties </li></ul></ul><ul><ul><li>Structures </li></ul></ul><ul><ul><li>Spectra </li></ul></ul><ul><li>Curation of existing data </li></ul>
  47. 47. Spectra
  48. 48. ChemSpider SyntheticPages
  49. 49. Submission Process <ul><li>Simple template-based submission process </li></ul><ul><li>Submissions reviewed by editorial board. Published as is or comments sent to author </li></ul><ul><li>Online Peer Review process </li></ul><ul><li>Data supported include web movies, images, live spectra etc. </li></ul><ul><li>DOI issued to author </li></ul>
  50. 50. Conclusion <ul><li>Diverse types of chemistry are available on the web </li></ul><ul><li>Searching of the internet is possible based on </li></ul><ul><ul><li>Text </li></ul></ul><ul><ul><li>Structure searching </li></ul></ul><ul><ul><li>Substructure searching </li></ul></ul><ul><li>The InChI has enabled linking on the internet </li></ul><ul><li>Quality on the Internet is diverse – separating the wheat from the chaff is not always easy! </li></ul><ul><li>It is possible to contribute to the chemistry internet! </li></ul>
  51. 51. Thank you Email: williamsa@rsc.org Twitter: ChemConnector Blog: www.chemspider.com/blog Personal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

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