Feeding and consuming data tosupport Open Notebook Science via          the ChemSpider PlatformAntony Williams, Jean-Claud...
Setting the Stage Chemists want access to tools and data     The more capabilities the better     The more data the bet...
Setting the Stage Chemists have access to tools and data     The more capabilities the better – we’ll see     The more ...
Welcome to ChemSpider 5 years, 28 million chemicals, linking 400 data  sources and growing daily Hosted by the Royal Soc...
Why Use ChemSpider?
Why Use ChemSpider?
Why Use ChemSpider?
Why Use ChemSpider?
Why Use ChemSpider? LINKING OUT
Why Use ChemSpider?
Why Use ChemSpider
Why Use ChemSpider
Why Use ChemSpider
Why Use ChemSpider
What about Syntheses?
ChemSpider SyntheticPages
Work in Progress – 300k Reactions
Storing ONS Reactions Working with JC Bradley to host ONS reactions Linking directly back to ONS reactions What if the ...
What we have been asked for   “Allow us to grab data”   “Let us link”   “Give us web services to integrate”   “Can we ...
What we have been asked for   “Allow us to grab data”   “Let us link”   “Give us web services to integrate”   “Can we ...
Simple Linking to ChemSpider Link using ChemSpiderID http://www.chemspider.com/1234567
ChemSpider IDs Proliferating Now
Simple Querying Example http://  www.chemspider.com/Search.aspx?q=InChIKey=XXO
Or InChI, or SMILES http://www.chemspider.com/Search.aspx?q=InChI=1S  m1/s1 http://www.chemspider.com/Search.aspx?  q=Cl...
Better to provide APIs….
Various Flavors of API
Various Flavors of API
MANY Web Services for integration
Feeding ONS Data into ChemSpider ONS data can be deposited into ChemSpider and  linked out to the ONS pages Simply depos...
Feeding ONS Data into ChemSpider ONS Solubility Challenge
Feeding ONS Data into ChemSpider
So isn’t ONS all about ELNs? Open Notebook Science is about   Making records of research publicly available    online as...
Feeding ELN Data into ChemSpider Integrate e-Notebooks into ChemSpider   IDBS e-Workbook plug-in allows direct    deposi...
Feeding ELN Data into ChemSpider
How much data is lost? How many reactions in a thesis never get  published? How many spectra of common materials could b...
What could the future look like? “Publicly funded” research data flows onto the web Licensing is clear and NOT a challen...
Leaving the Stage Chemists have access to tools and data     The more capabilities the better – what’s missing?     The...
ChemSpider Mobile
New URLs to try out ChemSpider Reactions:  www.chemspider.com/reactions ChemSpider Validation and Standardization  Platf...
ChemSpider Google
ChemSpider Google
Acknowledgments RSC Cheminformatics team JC Bradley’s lab Daniel Lowe – reactions Commercial Software – GGA Software, ...
Thank youEmail: williamsa@rsc.orgBlog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams
Feeding and consuming data to support open notebook science via the chem spider platform
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Feeding and consuming data to support open notebook science via the chem spider platform

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We are all benefiting from a shift towards openness fed by Open Source, Open Standards, Open Data and Open Access. Open Notebook Science is likely the scientific revolution of the near term. As more scientists become comfortable with the concepts of openly sharing their experiments and data, often in near real time, we are seeing a shift to significant increases in the availability of new data that does not have to be extracted from publications but is available as data feeds that can be delivered to the community. This presentation will provide an overview of how the ChemSpider database from the RSC supports Open Notebook Science using programmatic access to both data and services and how ChemSpider ingests data feeds to mesh together with our existing database of over 27 million chemical compounds.

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Feeding and consuming data to support open notebook science via the chem spider platform

  1. 1. Feeding and consuming data tosupport Open Notebook Science via the ChemSpider PlatformAntony Williams, Jean-Claude Bradley, Andrew Lang and Valery Tkachenko ACS Philadelphia August 2012
  2. 2. Setting the Stage Chemists want access to tools and data  The more capabilities the better  The more data the better  And give us an API with that…  And it should be free…  And constantly updated…  And all data should be Open…  And make it fully Open Source…  And it needs to be on my mobile…
  3. 3. Setting the Stage Chemists have access to tools and data  The more capabilities the better – we’ll see  The more data the better – changing daily  And give us an API with that… - not just one  And it should be free… - sure  And constantly updated… - indeed..please help!  And all data should be Open…- licensing  And make it fully Open Source… - kinda, sorta  And it needs to be on my mobile… - sure
  4. 4. Welcome to ChemSpider 5 years, 28 million chemicals, linking 400 data sources and growing daily Hosted by the Royal Society of Chemistry An important part of our long term strategic vision Free to access With lots/most/all (?) of the functionality necessary to support chemists and Open Notebook Science…
  5. 5. Why Use ChemSpider?
  6. 6. Why Use ChemSpider?
  7. 7. Why Use ChemSpider?
  8. 8. Why Use ChemSpider?
  9. 9. Why Use ChemSpider? LINKING OUT
  10. 10. Why Use ChemSpider?
  11. 11. Why Use ChemSpider
  12. 12. Why Use ChemSpider
  13. 13. Why Use ChemSpider
  14. 14. Why Use ChemSpider
  15. 15. What about Syntheses?
  16. 16. ChemSpider SyntheticPages
  17. 17. Work in Progress – 300k Reactions
  18. 18. Storing ONS Reactions Working with JC Bradley to host ONS reactions Linking directly back to ONS reactions What if the links decay? Host all related ONS data – benefits of Openness! Future applications for RInChIs
  19. 19. What we have been asked for “Allow us to grab data” “Let us link” “Give us web services to integrate” “Can we store our data with you?” “Can you give us predictions to validate data?”
  20. 20. What we have been asked for “Allow us to grab data” “Let us link” “Give us web services to integrate” “Can we store our data with you?” “Can you give us predictions to validate data?” “Can you build us an ELN?”
  21. 21. Simple Linking to ChemSpider Link using ChemSpiderID http://www.chemspider.com/1234567
  22. 22. ChemSpider IDs Proliferating Now
  23. 23. Simple Querying Example http:// www.chemspider.com/Search.aspx?q=InChIKey=XXO
  24. 24. Or InChI, or SMILES http://www.chemspider.com/Search.aspx?q=InChI=1S m1/s1 http://www.chemspider.com/Search.aspx? q=Clc1ccc(cc1)C(O)=C3C(=O)C(=O)N([C@@H]3 c2cccc(F)c2)CCc5c4ccccc4nc5
  25. 25. Better to provide APIs….
  26. 26. Various Flavors of API
  27. 27. Various Flavors of API
  28. 28. MANY Web Services for integration
  29. 29. Feeding ONS Data into ChemSpider ONS data can be deposited into ChemSpider and linked out to the ONS pages Simply deposit structure(s) and links
  30. 30. Feeding ONS Data into ChemSpider ONS Solubility Challenge
  31. 31. Feeding ONS Data into ChemSpider
  32. 32. So isn’t ONS all about ELNs? Open Notebook Science is about  Making records of research publicly available online as it is recorded ONS is enabled by software tools and platforms  Keep the notebook of the researcher online with all raw and processed data as it is generated (close to or near real time)  Notebooks as Wikis, Commercial or Free ELNs published to the web (choose public/private – what data to expose)
  33. 33. Feeding ELN Data into ChemSpider Integrate e-Notebooks into ChemSpider  IDBS e-Workbook plug-in allows direct deposition of chemical structures  Can be extended to more ELN content  Spectra  Reactions  Properties etc.  Integration Video http://tinyurl.com/9xnprqr
  34. 34. Feeding ELN Data into ChemSpider
  35. 35. How much data is lost? How many reactions in a thesis never get published? How many spectra of common materials could be shared? How many properties are measured and lost? What stands in the way of sharing?  Is it technology?  Permissions? “The Boss”, Licensing? And yes – there are data quality issues but there is algorithmic checking and data curation to help
  36. 36. What could the future look like? “Publicly funded” research data flows onto the web Licensing is clear and NOT a challenge Machines are picking up data and depositing EXAMPLE project – Any interest?  Put your spectra/structure in folders (Dropbox)  ChemSpider robot scoops, processes and deposits – opportunity with JC Bradley  While processing also predicts spectra and compares for validation
  37. 37. Leaving the Stage Chemists have access to tools and data  The more capabilities the better – what’s missing?  The more data the better – anyone want to share?  And give us an API with that… - ask us for help  And it should be free… - it is  And constantly updated… - help annotate/curate  And all data should be Open…- licensing  And make it fully Open Source… - book chapter  And it needs to be on my mobile… - it is
  38. 38. ChemSpider Mobile
  39. 39. New URLs to try out ChemSpider Reactions: www.chemspider.com/reactions ChemSpider Validation and Standardization Platform: www.chemspider.com/cvsp ChemSpider Google: www.chemspider.com/google
  40. 40. ChemSpider Google
  41. 41. ChemSpider Google
  42. 42. Acknowledgments RSC Cheminformatics team JC Bradley’s lab Daniel Lowe – reactions Commercial Software – GGA Software, ACD/Labs, OpenEye Open Source Components
  43. 43. Thank youEmail: williamsa@rsc.orgBlog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams
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