Linking explicit and implicit knowledge
17
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
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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.
Transcript of Linking explicit and implicit knowledge
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
Problem
BuildingBlocks
Conclusion
Explicit or implicit? Names...
benzene3-[4-[3-(1-methyl-7-oxo-3-propyl-4H-pyrazolo[4,3-d]pyrimidin-5-yl)-4-propoxyphenyl]sulfonylpiperazin-1-yl]propanoicacidInChI=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
Problem
BuildingBlocks
Conclusion
Knowledge...
Solanum lycopersicum...
We model our world, but ...Knowledge is hidden inPDFsTransformations areneededLife is not uni- or bivariate,neither is knowledgeInformation Loss!
2010-05-30 Bioclipse & Proteochemometric Group - 3 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Knowledge Representation: InformationLoss
2010-05-30 Bioclipse & Proteochemometric Group - 4 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Linking Data?
http://rdf.openmolecules.net/
2010-05-30 Bioclipse & Proteochemometric Group - 5 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
But what about similarity?!?
identitity: owl:sameAsstereochemistry: rdf:seeAlso ?similar molecules: rdf:seeAlso, chem:hasHighTanimoto ?
2010-05-30 Bioclipse & Proteochemometric Group - 6 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
... Molecular reality...
1 000 000 000 000 000 000 000 000000 000 000 000 000 000 000 000000 000 000 000... and that just the chemical graphs ...
2010-05-30 Bioclipse & Proteochemometric Group - 7 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
OpenMolecules RDF: dereferenceable URI
http://rdf.openmolecules.net/
2010-05-30 Bioclipse & Proteochemometric Group - 8 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
The Chemistry Development Kit
A Family of ProjectsCDK-Taverna (chemoinformatics workflows)JChemPaint (semantic 2D editor)ChemoJava (GPL-ed extension)
Goalslibrary of cheminformatics algorithmseducational
UsageCDK: 100+ times cited in scientific literatureBioclipse, KNIME, Jumbo (CML), AMBIT, ...
C. Steinbeck et al., J.Chem.Inf.Comput.Sci, 2003C. Steinbeck et al., Curr.Pharm.Design, 2006
2010-05-30 Bioclipse & Proteochemometric Group - 9 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Bioclipse
O. Spjuth et al., BMC Bioinformatics 2007, 8:59
2010-05-30 Bioclipse & Proteochemometric Group - 10 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Integration
Servicesdatabases: PubChemweb servicesGoogle SpreadsheetsMyExperiment.org: BioclipseScripting LanguageTwitter, ...journals, ...
TechniquesSOAP, REST, XMPP, . . .Resource Description Frameworkdedicated APIs
2010-05-30 Bioclipse & Proteochemometric Group - 11 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Bioclipse-RDF
local RDF storageread/write RDF/XML, N3run 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
Problem
BuildingBlocks
Conclusion
QSAR Wizards
2010-05-30 Bioclipse & Proteochemometric Group - 13 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
MyExperiment: Bioclipse ScriptingLanguage
2010-05-30 Bioclipse & Proteochemometric Group - 14 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Bioclipse + OpenTox
REST interaction (using RDF/SPARQL)
listAlgorithms(String service);
listDescriptors(String service);
listDataSets(String service);
listCompounds(String service,Integer dataSet);
downloadCompoundAsMDLMolfile(String service, Integer dataSet,Integer compound);
downloadDataSetAsMDLSDfile(String service, Integer dataSet,String filename);
Needed
create, manipulatedata sets . . .
upload molecules
calculate descriptors
2010-05-30 Bioclipse & Proteochemometric Group - 15 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
Conclusions
Where did this take us?
Platform to integrate the RDF withthe computation world
Bioclipse as glue
Scripting, sharing of scripts withMyExperiment.org
What’s next?
Triple generation ondemand (XMPP,SADI, ...)
Ontology alignments
Semantic Mediawikiintegration
2010-05-30 Bioclipse & Proteochemometric Group - 16 - Egon Willighagen | chem-bla-ics.blogspot.com
Problem
BuildingBlocks
Conclusion
The Details
http://www.citeulike.org/user/
egonw/tag/papers
http:
//chem-bla-ics.blogspot.com
http://egonw.github.com
waveto:
2010-05-30 Bioclipse & Proteochemometric Group - 17 - Egon Willighagen | chem-bla-ics.blogspot.com
