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Chemical InteroperabilityEgon WillighagenBiGCaT – Dept of Bioinformatics2012-02-17, Utrecht
Interoperability in Chemistry• = Communication, meaning• Why?  – Reproducibility  – Understanding molecular properties• In...
Whats that Open fetish?• Gives  – Collaboration. Credit. Ownership.  – Sustainability.• Trough rights  – Redistribution (u...
The Blue Obelisk MovementR. Guha et al. J. Chem. Inf. Mod. 2006N. OBoyle et al. J. Cheminf. 2011
1. Open Standards• Allows:  – Software to talk to each other• For:  – Well-defined formats  – Concepts (aromaticity!)  – P...
CML: Exchange of Chemical StructuresP. Murray-Rust et al, J. Chem. Inf. Comput. Sci., 1999E.L. Willighagen, Internet J. Ch...
CML in RSS news feedsP. Murray-Rust et al., J. Chem. Inf. Comput. Sci, 2004
Resource Description Framework• Family of W3C technologies  – RDF / RDFS: basic framework  – Serialization formats    • RD...
SemanticWeb
IUPAC International Chemical IdentifierN. Day. InChI FAQ, http://wwmm.ch.cam.ac.uk/inchifaq/
2. Open Data• What is the average C=N bond length?  – Bioinformatics: force fields• What is the LogP of aspirin?  – Drug d...
Linked Open Drug DataM. Samwald et al., J. Cheminf, 2011
Blue Obelisk Data Repository●    Which two tools calculate the same    molecular weight?●    Isotope abundancies and weigh...
3. Open Source• What is aromaticity?
Chemistry Development Kit• Cheminformatics     – Aromaticity     – ...• Many derived tools     – Taverna, KNIME, Bioclipse...
Scripting ...O. Spjuth et al. BMC Bioinf. 2009T. Kuhn et al. BMC Bioinf. 2010
Predictive Toxicology IO. Spjuth et al. J. Chem. Inf. Mod. 2011E.L. Willighagen et al. BMC Research Notes. 2011
Predictive Toxicology IIE.L. Willighagen et al. J. Biomed Sem. 2011
Conclusions• Interoperability via ODOSOS  – Open Data  – Open Standards  – Open Source
Thanx / More info• Blue Obelisk movement• CDK developers (Miguel!)• http://scholar.google.com/citations?user=u8SjMZ0AAAAJ•...
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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.

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Transcript of "Chemical Interoperability - Utrecht / NBIC"

  1. 1. Chemical InteroperabilityEgon WillighagenBiGCaT – Dept of Bioinformatics2012-02-17, Utrecht
  2. 2. Interoperability in Chemistry• = Communication, meaning• Why? – Reproducibility – Understanding molecular properties• Interoperability Needs – Open Data, Open Standards, Open Source
  3. 3. Whats that Open fetish?• Gives – Collaboration. Credit. Ownership. – Sustainability.• Trough rights – Redistribution (under same rights) – Modification (not with Open Standards)
  4. 4. The Blue Obelisk MovementR. Guha et al. J. Chem. Inf. Mod. 2006N. OBoyle et al. J. Cheminf. 2011
  5. 5. 1. Open Standards• Allows: – Software to talk to each other• For: – Well-defined formats – Concepts (aromaticity!) – Practices (licenses, peer review, ...)
  6. 6. CML: Exchange of Chemical StructuresP. Murray-Rust et al, J. Chem. Inf. Comput. Sci., 1999E.L. Willighagen, Internet J. Chem., 2000
  7. 7. CML in RSS news feedsP. Murray-Rust et al., J. Chem. Inf. Comput. Sci, 2004
  8. 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. 9. SemanticWeb
  10. 10. IUPAC International Chemical IdentifierN. Day. InChI FAQ, http://wwmm.ch.cam.ac.uk/inchifaq/
  11. 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. 12. Linked Open Drug DataM. Samwald et al., J. Cheminf, 2011
  13. 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. 14. 3. Open Source• What is aromaticity?
  15. 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. 16. Scripting ...O. Spjuth et al. BMC Bioinf. 2009T. Kuhn et al. BMC Bioinf. 2010
  17. 17. Predictive Toxicology IO. Spjuth et al. J. Chem. Inf. Mod. 2011E.L. Willighagen et al. BMC Research Notes. 2011
  18. 18. Predictive Toxicology IIE.L. Willighagen et al. J. Biomed Sem. 2011
  19. 19. Conclusions• Interoperability via ODOSOS – Open Data – Open Standards – Open Source
  20. 20. Thanx / More info• Blue Obelisk movement• CDK developers (Miguel!)• http://scholar.google.com/citations?user=u8SjMZ0AAAAJ• http://chem-bla-ics.blogspot.com/
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