ChemSpider reactions – delivering a free community resource of chemical syntheses
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Transcript of ChemSpider reactions – delivering a free community resource of chemical syntheses
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ChemSpider Reactions: Delivering a free community
resource of chemical syntheses
Valery Tkachenko, Colin Batchelor, Daniel Lowe, Ken Karapetyan, David Sharpe and Antony Williams
ACS New Orleans April 2013
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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
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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.
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RSC and chemical reaction data 1
Graphical abstracting journals:Methods in Organic Synthesis (monthly, 1990 to present)Catalysts and Catalysed Reactions (monthly, 2005 to present)
These constitute a backfile of over 50000 novel reactions
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RSC and chemical reaction data 2
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RSC and chemical reaction data 3
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New sources of reaction data
Daniel Lowe’s PhD thesis (Cantab, 2012) was on extracting reactions from US patent data.We can apply this technology to the RSC Journal archive.
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ChemSpider Reactionsbringing it all together
http://csr.dev.rsc-us.org/
WORK IN PROGRESS
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Reaction classification 1
Project Prospect has text-mined RSC journal articles for named reactions and molecular processes, annotated according to Creative Commons-licensed ontologies:
See http://rxno.googlecode.com/
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Reaction classification 2
Classification of Daniel’s US Patent data
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Reaction InChI
To do for reactions what InChI has done for structures•Think online searching•Deduplication and linking
http://www-rinchi.ch.cam.ac.uk/help.html
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Reaction InChIEarly work – RInChIs layered on to a few hundred thousand reactions •Not generated for a few 10s of thousands of reactions •Reaction deduplication results differ based on algorithm – GGA software versus RInChI•Under investigation
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Other sources
ChemSpider SyntheticPages
•Electronic Lab Notebooks•University repositories
Please send theses
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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)
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Chemical Database ServiceNational Chemical Database Service for UK academicsIntegrates commercial databases and servicesChemicals, analytical data, prediction algorithmsDevelopment of data repository
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ARChem from SimBioSys 1
Synthesis planning tool which performs rule- and precedent-based retrosynthetic analysis back to commercially available starting materials.
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ARChem from SimBiosys 2
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ARChem from SimBioSys 3
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But what about data quality?
• Data validation and curation required• Encouraging participation with
Rewards and RECOGNITION
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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
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The other kind of RDF(made-up example)
Chemical reactions are unusually well-suited to representation. (Donald Davidson’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> .