ChemSpider reactions – delivering a free community resource of chemical syntheses

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Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013. …

Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013.

There are dozens of public compound databases now available online, some of these providing access to tens of millions of chemical compounds. However, very little effort has been put into the delivery of databases of chemical reactions with the majority of large resources being commercial in nature. In our five years of delivering chemical based data resources to the chemistry community one of the primary requests has been that chemists want to know how to synthesize many of the chemicals they are researching. This presentation will provide an overview of our concerted efforts to enhance access to freely available chemistry data and will discuss the ChemSpider Reactions as an integrating hub of content including data extracted from US patents, from RSC Journals and databases and from our micro-publishing platform ChemSpider Synthetic Pages (CSSP).

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  • 1. ChemSpider Reactions: Delivering a free communityresource of chemical synthesesValery Tkachenko, Colin Batchelor, Daniel Lowe, Ken Karapetyan, David Sharpe and Antony Williams ACS New Orleans April 2013
  • 2. Overview• Motivation• The RSC and chemical reaction data• New sources of chemical reaction data• ChemSpider Reactions: bringing it all together• Experiments with reaction classification• The National Chemical Database Service
  • 3. Who needs another reaction database?• Those who cannot afford to license access…• Those who would like to access data that is not abstracted• Those who might like to contribute data to a database• Anybody wanting to integrate their systems in and to pull data out.
  • 4. RSC and chemical reaction data 1Graphical abstracting journals:Methods in Organic Synthesis (monthly, 1990 to present)Catalysts and Catalysed Reactions (monthly, 2005 topresent)These constitute a backfile of over 50000 novel reactions
  • 5. RSC and chemical reaction data 2
  • 6. RSC and chemical reaction data 3
  • 7. New sources of reaction dataDaniel Lowe’s PhD thesis (Cantab, 2012) was onextracting reactions from US patent data.We can apply this technology to the RSC Journalarchive.
  • 8. ChemSpider Reactions bringing it all togetherhttp://csr.dev.rsc-us.org/WORK IN PROGRESS
  • 9. Reaction classification 1Project Prospect has text-mined RSC journalarticles for named reactions and molecularprocesses, annotated according to CreativeCommons-licensed ontologies:See http://rxno.googlecode.com/
  • 10. Reaction classification 2Classification of Daniel’s USPatent data
  • 11. Reaction InChITo do for reactions what InChI has done forstructures•Think online searching•Deduplication and linkinghttp://www-rinchi.ch.cam.ac.uk/help.html
  • 12. Reaction InChIEarly work – RInChIs layered on to a fewhundred thousand reactions•Not generated for a few 10s of thousands ofreactions•Reaction deduplication results differ based onalgorithm – GGA software versus RInChI•Under investigation
  • 13. Other sourcesChemSpider SyntheticPages•Electronic Lab Notebooks•University repositoriesPlease send theses
  • 14. What will ChemSpider Reactions serve?• Chemical Database Service• Linking back to original publications/supplementary data• Underpinning other tools e.g. retrosynthetic analysis (depends on data quality and mapping)
  • 15. Chemical DatabaseServiceNational Chemical Database Servicefor UK academicsIntegrates commercial databases andservicesChemicals, analytical data, predictionalgorithmsDevelopment of data repository
  • 16. ARChem from SimBioSys 1Synthesis planning tool which performs rule-and precedent-based retrosynthetic analysisback to commercially available startingmaterials.
  • 17. ARChem from SimBiosys 2
  • 18. ARChem from SimBioSys 3
  • 19. But what about data quality?• Data validation and curation required• Encouraging participation with Rewards and RECOGNITION
  • 20. Manual curation• Integrated commenting, curating and validation platform across ALL eScience and Publishing platforms• All integrated to a central RSC profile and feeding the alt-metrics tools
  • 21. The other kind of RDF (made-up example)Chemical reactions are unusually well-suited to representation. (DonaldDavidson’s event semantics)_:r1 a obo:RXNO_0000004 ; # Diels–Alder obo:has_participant_ceasing_to_exist _:m1 ;# a diene obo:has_participant_ceasing_to_exist _:m2 ;# an olefin obo:has_participant_starting_to_exist _:m3 .# a substituted cyclohexene_:m1 a <http://rdf.chemspider.com/233000> ._:m2 a <http://rdf.chemspider.com/233001> ._:m3 a <http://rdf.chemspider.com/233002> .
  • 22. Questions?E-mail: tkachenkov@rsc.org, batchelorc@rsc.org