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Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
Linking Open Drug Data to Cheminformatics and Proteochemometrics
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Linking Open Drug Data to Cheminformatics and Proteochemometrics

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My talk at SWAT4LS 2009 in Amsterdam.

My talk at SWAT4LS 2009 in Amsterdam.

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  • 1. Linking Open Drug Data to Cheminformatics and Proteochemometrics Egon Willighagen <http://chem-bla-ics.blogspot.com/> Bioclipse & Proteochemometric Group (Prof. Wikberg) Department of Pharmaceutical Biosciences Uppsala University 2009-11-20
  • 2. Knowledge... We model our world, but ... Life is not uni- or bivariate Knowledge is not either But we think of it as such Information Loss! Solanum lycopersicum... 2009-11-20 Bioclipse & Proteochemometric Group -2- Egon Willighagen | chem-bla-ics.blogspot.com
  • 3. Names... benzene 3-[4-[3-(1-methyl-7-oxo-3-propyl-4H- pyrazolo[4,3-d]pyrimidin-5-yl)-4- propoxyphenyl]sulfonylpiperazin-1- yl]propanoic acid InChI=1S/C25H34N6O6S/c1-4-6-19-22- 23(29(3)28-19)25(34)27-24(26-22)18-16- 17(7-8-20(18)37-15-5-2)38(35,36)31-13-11- 30(12-14-31)10-9-21(32)33/h7-8,16H,4-6,9- 15H2,1-3H3,(H,32,33)(H,26,27,34) 2009-11-20 Bioclipse & Proteochemometric Group -3- Egon Willighagen | chem-bla-ics.blogspot.com
  • 4. ... Molecular reality... 1 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 2009-11-20 Bioclipse & Proteochemometric Group -4- Egon Willighagen | chem-bla-ics.blogspot.com
  • 5. ... and Numbers 2009-11-20 Bioclipse & Proteochemometric Group -5- Egon Willighagen | chem-bla-ics.blogspot.com
  • 6. Knowledge Representation: Information Loss 2009-11-20 Bioclipse & Proteochemometric Group -6- Egon Willighagen | chem-bla-ics.blogspot.com
  • 7. Data Analysis 2009-11-20 Bioclipse & Proteochemometric Group -7- Egon Willighagen | chem-bla-ics.blogspot.com
  • 8. Proteochemometrics 2009-11-20 Bioclipse & Proteochemometric Group -8- Egon Willighagen | chem-bla-ics.blogspot.com
  • 9. Main Theme How do we navigate dimensionality space? How include prior knowledge? While minimizing information loss? With optimal knowledge extraction? And maximizing interpretability? Without ending up in random correlation? 2009-11-20 Bioclipse & Proteochemometric Group -9- Egon Willighagen | chem-bla-ics.blogspot.com
  • 10. OpenMolecules RDF: dereferenceable URI http://rdf.openmolecules.net/ 2009-11-20 Bioclipse & Proteochemometric Group - 10 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 11. OpenMolecules RDF: linked data http://rdf.openmolecules.net/ 2009-11-20 Bioclipse & Proteochemometric Group - 11 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 12. The Chemistry Development Kit A Family of Projects CDK-Taverna (chemoinformatics workflows) JChemPaint (semantic 2D editor) ChemoJava (GPL-ed extension) Goals library of cheminformatics algorithms educational Usage CDK: 100+ times cited in scientific literature Bioclipse, KNIME, Jumbo (CML), AMBIT, ... C. Steinbeck et al., J.Chem.Inf.Comput.Sci, 2003 C. Steinbeck et al., Curr.Pharm.Design, 2006 2009-11-20 Bioclipse & Proteochemometric Group - 12 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 13. Bioclipse O. Spjuth et al., BMC Bioinformatics 2007, 8:59 2009-11-20 Bioclipse & Proteochemometric Group - 13 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 14. Integration Services databases: PubChem web services Google Spreadsheets MyExperiment.org: Bioclipse Scripting Language Twitter, ... journals, ... Techniques SOAP, REST, XMPP, . . . Resource Description Framework dedicated APIs 2009-11-20 Bioclipse & Proteochemometric Group - 14 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 15. Bioclipse-RDF local RDF storage read/write RDF/XML, N3 run SPARQL queries (local and remote) extract RDF from XHTML/RDFa Thanx to Jena and Pellet. 2009-11-20 Bioclipse & Proteochemometric Group - 15 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 16. Quote of the Day "There are too many people doing data integration, this is a waste of a lot of smart people’s time" @alanruttenberg at #swat4ls2009 via dullhunk - twitter 2009-11-20 Bioclipse & Proteochemometric Group - 16 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 17. SPARQL end points GNU FDL NMRShiftDB data (also available via Bio2RDF) CC0 ChemPedia Open Notebook Science Solubility 2009-11-20 Bioclipse & Proteochemometric Group - 17 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 18. Names 2 Graphs 2 Numbers... 2009-11-20 Bioclipse & Proteochemometric Group - 18 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 19. Disease 2 PDB 2009-11-20 Bioclipse & Proteochemometric Group - 19 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 20. CDK as RDF model1:atom1 a cdk:Atom ; cdk:hasFormalCharge "1" ; cdk:symbol "O" . model1:atom2 a cdk:Atom ; cdk:symbol "C" . model1:mol1 a cdk:Molecule ; dc:title "Methanol" ; owl:sameAs <http://rdf.openmolecules.net/?InChI=1/CH4O/c1-2 cdk:hasAtom model1:atom2 , model1:atom1 ; cdk:hasBond model1:bond1 . 2009-11-20 Bioclipse & Proteochemometric Group - 20 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 21. Proteochemometrics 2009-11-20 Bioclipse & Proteochemometric Group - 21 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 22. OWL for Descriptors Used for model and data. 2009-11-20 Bioclipse & Proteochemometric Group - 22 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 23. MyExperiment: Bioclipse Scripting Language 2009-11-20 Bioclipse & Proteochemometric Group - 23 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 24. What does this bring us? Platform to integrate the RDF with the computation world Bioclipse as single point of access Scripting, sharing of scripts with MyExperiment.org Bridge the nominal with the numerical world 2009-11-20 Bioclipse & Proteochemometric Group - 24 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 25. Where next? Framework Triple generation on demand (XMPP, SADI, ...) Ontology alignments Semantic Mediawiki integration Proteochemometrics Knowledge discovery Data set aggregation Automated model validation 2009-11-20 Bioclipse & Proteochemometric Group - 25 - Egon Willighagen | chem-bla-ics.blogspot.com
  • 26. The Details http://www.citeulike.org/user/ egonw/tag/papers http: //chem-bla-ics.blogspot.com http://egonw.github.com waveto: egon.willighagen@googlewave.com 2009-11-20 Bioclipse & Proteochemometric Group - 26 - Egon Willighagen | chem-bla-ics.blogspot.com

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