Linking explicit and implicit knowledge

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My views on how various levels of 'scientific knowledge' should be linked for a 15min OpenTox Workshop talk, in Potsdam, 30 May 2010.

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Linking explicit and implicit knowledge

  1. 1. Linking explicit and implicit knowledge Egon Willighagen <http://chem-bla-ics.blogspot.com/> Bioclipse & Proteochemometric Group (Prof. Wikberg) Department of Pharmaceutical Biosciences Uppsala University 2010-05-30
  2. 2. Explicit or implicit? Names... Problem benzene Building 3-[4-[3-(1-methyl-7-oxo-3-propyl-4H- Blocks pyrazolo[4,3-d]pyrimidin-5-yl)-4- Conclusion 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) 2010-05-30 Bioclipse & Proteochemometric Group -2- Egon Willighagen | chem-bla-ics.blogspot.com
  3. 3. Knowledge... Problem Building We model our world, but ... Blocks Knowledge is hidden in Conclusion PDFs Transformations are needed Life is not uni- or bivariate, neither is knowledge Information Loss! Solanum lycopersicum... 2010-05-30 Bioclipse & Proteochemometric Group -3- Egon Willighagen | chem-bla-ics.blogspot.com
  4. 4. Knowledge Representation: Information Loss Problem Building Blocks Conclusion 2010-05-30 Bioclipse & Proteochemometric Group -4- Egon Willighagen | chem-bla-ics.blogspot.com
  5. 5. Linking Data? Problem Building Blocks Conclusion http://rdf.openmolecules.net/ 2010-05-30 Bioclipse & Proteochemometric Group -5- Egon Willighagen | chem-bla-ics.blogspot.com
  6. 6. But what about similarity?!? Problem Building Blocks Conclusion identitity: owl:sameAs stereochemistry: rdf:seeAlso ? similar molecules: rdf:seeAlso, chem:hasHighTanimoto ? 2010-05-30 Bioclipse & Proteochemometric Group -6- Egon Willighagen | chem-bla-ics.blogspot.com
  7. 7. ... Molecular reality... 1 000 000 000 000 000 000 000 000 Problem 000 000 000 000 000 000 000 000 Building Blocks 000 000 000 000 Conclusion ... and that just the chemical graphs ... 2010-05-30 Bioclipse & Proteochemometric Group -7- Egon Willighagen | chem-bla-ics.blogspot.com
  8. 8. OpenMolecules RDF: dereferenceable URI Problem Building Blocks Conclusion http://rdf.openmolecules.net/ 2010-05-30 Bioclipse & Proteochemometric Group -8- Egon Willighagen | chem-bla-ics.blogspot.com
  9. 9. The Chemistry Development Kit A Family of Projects CDK-Taverna (chemoinformatics workflows) Problem Building JChemPaint (semantic 2D editor) Blocks ChemoJava (GPL-ed extension) Conclusion 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 2010-05-30 Bioclipse & Proteochemometric Group -9- Egon Willighagen | chem-bla-ics.blogspot.com
  10. 10. Bioclipse Problem Building Blocks Conclusion O. Spjuth et al., BMC Bioinformatics 2007, 8:59 2010-05-30 Bioclipse & Proteochemometric Group - 10 - Egon Willighagen | chem-bla-ics.blogspot.com
  11. 11. Integration Services databases: PubChem Problem Building web services Blocks Google Spreadsheets Conclusion MyExperiment.org: Bioclipse Scripting Language Twitter, ... journals, ... Techniques SOAP, REST, XMPP, . . . Resource Description Framework dedicated APIs 2010-05-30 Bioclipse & Proteochemometric Group - 11 - Egon Willighagen | chem-bla-ics.blogspot.com
  12. 12. Bioclipse-RDF Problem Building Blocks Conclusion local RDF storage read/write RDF/XML, N3 run SPARQL queries (local and remote) extract RDF from XHTML/RDFa Thanx to Jena and Pellet. 2010-05-30 Bioclipse & Proteochemometric Group - 12 - Egon Willighagen | chem-bla-ics.blogspot.com
  13. 13. QSAR Wizards Problem Building Blocks Conclusion 2010-05-30 Bioclipse & Proteochemometric Group - 13 - Egon Willighagen | chem-bla-ics.blogspot.com
  14. 14. MyExperiment: Bioclipse Scripting Language Problem Building Blocks Conclusion 2010-05-30 Bioclipse & Proteochemometric Group - 14 - Egon Willighagen | chem-bla-ics.blogspot.com
  15. 15. Bioclipse + OpenTox REST interaction (using RDF/SPARQL) Problem listAlgorithms(String service); Building Blocks listDescriptors(String service); Conclusion Needed listDataSets(String service); create, manipulate listCompounds(String service, data sets . . . Integer dataSet); upload molecules downloadCompoundAsMDLMolfile( String service, Integer dataSet, calculate descriptors Integer compound); downloadDataSetAsMDLSDfile( String service, Integer dataSet, String filename); 2010-05-30 Bioclipse & Proteochemometric Group - 15 - Egon Willighagen | chem-bla-ics.blogspot.com
  16. 16. Conclusions Problem Building What’s next? Blocks Where did this take us? Triple generation on Conclusion Platform to integrate the RDF with demand (XMPP, the computation world SADI, ...) Bioclipse as glue Ontology alignments Scripting, sharing of scripts with Semantic Mediawiki MyExperiment.org integration 2010-05-30 Bioclipse & Proteochemometric Group - 16 - Egon Willighagen | chem-bla-ics.blogspot.com
  17. 17. The Details Problem Building Blocks http://www.citeulike.org/user/ Conclusion egonw/tag/papers http: //chem-bla-ics.blogspot.com http://egonw.github.com waveto: egon.willighagen@googlewave.com 2010-05-30 Bioclipse & Proteochemometric Group - 17 - Egon Willighagen | chem-bla-ics.blogspot.com

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