Linking Open Drug Data toCheminformatics andProteochemometrics

Egon Willighagen <http://chem-bla-ics.blogspot.com/>

Bioclipse & Proteochemometric Group (Prof. Wikberg)Department of Pharmaceutical Biosciences

Uppsala University

2009-11-20

Knowledge...

Solanum lycopersicum...

We model our world, but ...Life is not uni- or bivariateKnowledge is not eitherBut we think of it as suchInformation Loss!

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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)

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... Molecular reality...

1 000 000 000 000 000 000 000 000000 000 000 000 000 000 000 000000 000 000 000

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... and Numbers

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Knowledge Representation: InformationLoss

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Data Analysis

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Proteochemometrics

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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?

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OpenMolecules RDF: dereferenceable URI

http://rdf.openmolecules.net/

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OpenMolecules RDF: linked data

http://rdf.openmolecules.net/

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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

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Bioclipse

O. Spjuth et al., BMC Bioinformatics 2007, 8:59

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Integration

Servicesdatabases: PubChemweb servicesGoogle SpreadsheetsMyExperiment.org: BioclipseScripting LanguageTwitter, ...journals, ...

TechniquesSOAP, REST, XMPP, . . .Resource Description Frameworkdedicated APIs

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Bioclipse-RDF

local RDF storageread/write RDF/XML, N3run SPARQL queries (local and remote)extract RDF from XHTML/RDFa

Thanx to Jena and Pellet.

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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

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SPARQL end points

GNU FDLNMRShiftDB data (also available via Bio2RDF)

CC0ChemPediaOpen Notebook Science Solubility

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Names 2 Graphs 2 Numbers...

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Disease 2 PDB

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CDK as RDF

model1:atom1a cdk:Atom ;cdk:hasFormalCharge "1" ;cdk:symbol "O" .

model1:atom2a cdk:Atom ;cdk:symbol "C" .

model1:mol1a cdk:Molecule ;dc:title "Methanol" ;owl:sameAs <http://rdf.openmolecules.net/?InChI=1/CH4O/c1-2/h2H,1H3> ;cdk:hasAtom model1:atom2 ,

model1:atom1 ;cdk:hasBond model1:bond1 .

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Proteochemometrics

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OWL for Descriptors

Used for model and data.

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MyExperiment: Bioclipse ScriptingLanguage

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What does this bring us?

Platform to integrate the RDF with the computation worldBioclipse as single point of accessScripting, sharing of scripts with MyExperiment.orgBridge the nominal with the numerical world

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Where next?

FrameworkTriple generation on demand (XMPP, SADI, ...)Ontology alignmentsSemantic Mediawiki integration

ProteochemometricsKnowledge discoveryData set aggregationAutomated model validation

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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

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