Oops and Downs of Resolving InChIs For the Chemistry Community

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    Oops and Downs of Resolving InChIs For the Chemistry Community - Presentation Transcript

    1. Oops and downs of resolving InChIs for the chemistry community
    2. The InChI Has Arrived
      • My opinions :
      • The InChI is a crucial part of the future of structure-based relationships on the web
      • The semantic web of chemistry will sit on the shoulders of InChI until there is something better
      • InChIs and publishers are already in relationship – publishers who have not adopted will follow
    3. PPP – Perfection vs Productive vs Prolific
      • The InChI is not perfect
      • There are limitations but they are acknowledged and in discussion
      • The InChI is very “productive”
      • InChIs are showing up in databases, manuscripts, spreadsheets, on publications, in software
    4. A Lot of Variability in InChIs
      • Source: Unofficial InChI FAQ page
    5. InChIStrings Hash to InChIKeys
    6. HVYWMOMLDIMFJA-DPAQBDIFSA-N
    7. The InChI Resolver
    8. Inchis.chemspider.com
    9. Resolve an InChI or InChIKey
    10. Resolved
    11. Connection Only Resolving
    12. InChIs and Big Databases
      • There appears to be a bigger is better mentality with online databases
      • InChI has shown a lot of “overlap” in the ChemSpider database
      • Distinction : a unique chemical entity versus what it’s meant to be
      • Some simple examples …
    13. Spot The Difference
    14. Standard InChIKeys
    15. Spot The Difference
    16. 55 Hits in 0.08 Seconds
    17. Large Databases Contain Junk
      • InChI Resolvers will get us back to results but it’s a look up..
      • There is an enormous need for curation and linking resolved structures to “correct” structures – a manual task
    18. Generate-It
    19. Draw and generate
    20. Generate
    21. All Flavors
    22. Historical and Future InChIs
      • The Standard InChI removed variability
      • There will be new variants in the future
      • There are already millions of historical InChIs “out there”
      • Resolvers should accommodate historical and future InChIs
    23. In Our Resolver…
    24. On to ChemSpider…
    25. NEW Patents and Pubmed on ChemSpider
    26. InChIs to Patents and Pubmed Articles
    27. But there will be multiple resolvers…
      • Each publisher, database, scientist can choose not to publish their structures into a centralized database
      • There are many large online databases. There is no need to merge/mirror them – each can be a resolver
      • They need to be federated
    28. Many ways to address resolving
      • Our approach is simple – lookup. We look up the structure. SIMPLE.
    29. NCI/CADD resolver: 69 million structures
    30. Differences
      • The NCI and ChemSpider Resolvers are “different”
        • Different databases behind the resolver – Feedback from NCI: “Preliminary results indicate that inchis.chemspider.com can resolve approx. 28% of our structures.”
        • Our approaches for resolving differ
        • Some features are different
    31. The InChI Resolver Protocol
      • There will not be only one InChI Resolver – there will be many
        • Publishers
        • Commercial Databases
        • Free services and resources : PubChem, ChemSpider, NCI Database, ChEBI
      • Resolvers will not be mirrors of each other
        • There is no need to mirror when a protocol is in place
    32. InChI Resolver Protocol
      • InChI resolving needs to be federated
      • A common protocol can connect resolvers so that a user gets a complete results set
      • Individual resolvers can have different capabilities but an agreed common protocol for resolving InChIs
    33. Discuss with us on Google Groups
      • Draft protocol for ACS Spring 2010 from
        • RSC ChemSpider
        • NCI/CADD
        • PubChem
        • Symyx
      • Proof of concept hopefully by end of this year for initial feedback (NCI and ChemSpider
      • Join us at http://tinyurl.com/r7q9zc http://groups.google.com/group/inchiresolverprotocol
    34. InChI trust
      • The founder members of the Trust: Elsevier, Thompson Reuters, Wiley, Nature Publishing Group, Royal Society of Chemistry, Symyx, FIZ-Chemie, Taylor & Francis and OpenEye
    35. In InChIs We Trust
      • It was said….
        • “ There is a finite, but very small probability of finding two structures with the same InChIKey.”
        • The first collision was announced on Sunday by Jonathan Goodman
    36. Spongistatin
    37. Probabilities are what they are…
      • “ The molecule for which a collision has been reported … gives rise to 2 26 = 67,108,864 possible stereoisomers”
      • The probability of a clash is low but finite…and it happened.
      • OR…there may be a bug…work underway
    38. The Future
      • InChI is here
      • InChIKeys are proliferating
      • The need for lookup is inevitable – the need for federated resolvers is obvious
      • Intention to provide draft resolver protocol by end of year
      • ACS Spring – unveil proof of concept
    39. Acknowledgments
      • The InChI “Team” – leadership team, developers, advisors, funders and the community providing feedback
      • Royal Society of Chemistry
    40. Thank you [email_address] Twitter: ChemSpiderman www.chemspider.com/blog
    SlideShare Zeitgeist 2009

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