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Chemical Interoperability - Utrecht / NBIC


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Presentation given at a parallel NBIC meeting in Utrecht at 17 Feb 2012. This presentation is not Open; figures are available from cited papers.

Presentation given at a parallel NBIC meeting in Utrecht at 17 Feb 2012. This presentation is not Open; figures are available from cited papers.

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  • 1. Chemical InteroperabilityEgon WillighagenBiGCaT – Dept of Bioinformatics2012-02-17, Utrecht
  • 2. Interoperability in Chemistry• = Communication, meaning• Why? – Reproducibility – Understanding molecular properties• Interoperability Needs – Open Data, Open Standards, Open Source
  • 3. Whats that Open fetish?• Gives – Collaboration. Credit. Ownership. – Sustainability.• Trough rights – Redistribution (under same rights) – Modification (not with Open Standards)
  • 4. The Blue Obelisk MovementR. Guha et al. J. Chem. Inf. Mod. 2006N. OBoyle et al. J. Cheminf. 2011
  • 5. 1. Open Standards• Allows: – Software to talk to each other• For: – Well-defined formats – Concepts (aromaticity!) – Practices (licenses, peer review, ...)
  • 6. CML: Exchange of Chemical StructuresP. Murray-Rust et al, J. Chem. Inf. Comput. Sci., 1999E.L. Willighagen, Internet J. Chem., 2000
  • 7. CML in RSS news feedsP. Murray-Rust et al., J. Chem. Inf. Comput. Sci, 2004
  • 8. Resource Description Framework• Family of W3C technologies – RDF / RDFS: basic framework – Serialization formats • RDF/XML, Turtle, RDFa, RDF/JSON – OWL: ontologies (BioPortal, OLS, …) – SPARQL
  • 9. SemanticWeb
  • 10. IUPAC International Chemical IdentifierN. Day. InChI FAQ,
  • 11. 2. Open Data• What is the average C=N bond length? – Bioinformatics: force fields• What is the LogP of aspirin? – Drug discovery• What metabolite is that? – Metabolomics
  • 12. Linked Open Drug DataM. Samwald et al., J. Cheminf, 2011
  • 13. Blue Obelisk Data Repository● Which two tools calculate the same molecular weight?● Isotope abundancies and weights! ● IUPAC reportsR. Guha et al. J. Chem. Inf. Mod. 2006
  • 14. 3. Open Source• What is aromaticity?
  • 15. Chemistry Development Kit• Cheminformatics – Aromaticity – ...• Many derived tools – Taverna, KNIME, Bioclipse, Cinfony, ...C. Steinbeck et al. J. Chem. Inf. Mod. 2003C. Steinbeck et al. Curr. Pharm. Des. 2006
  • 16. Scripting ...O. Spjuth et al. BMC Bioinf. 2009T. Kuhn et al. BMC Bioinf. 2010
  • 17. Predictive Toxicology IO. Spjuth et al. J. Chem. Inf. Mod. 2011E.L. Willighagen et al. BMC Research Notes. 2011
  • 18. Predictive Toxicology IIE.L. Willighagen et al. J. Biomed Sem. 2011
  • 19. Conclusions• Interoperability via ODOSOS – Open Data – Open Standards – Open Source
  • 20. Thanx / More info• Blue Obelisk movement• CDK developers (Miguel!)••