Linking Open Drug Data to Cheminformatics and Proteochemometrics

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

http://chem-bla-ics.blogspot.com/

Knowledge...

Solanum lycopersicum...

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

2009-11-20 Bioclipse & Proteochemometric Group - 2 - Egon Willighagen | chem-bla-ics.blogspot.com

chem-bla-ics.blogspot.com

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)



... Molecular reality...

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



... and Numbers



Knowledge Representation: InformationLoss



Data Analysis



Proteochemometrics



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?



OpenMolecules RDF: dereferenceable URI

http://rdf.openmolecules.net/




OpenMolecules RDF: linked data





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



Bioclipse

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



Integration

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

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



Bioclipse-RDF

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

Thanx to Jena and Pellet.



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



SPARQL end points

GNU FDLNMRShiftDB data (also available via Bio2RDF)

CC0ChemPediaOpen Notebook Science Solubility



Names 2 Graphs 2 Numbers...



Disease 2 PDB



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 .



Proteochemometrics



OWL for Descriptors

Used for model and data.



MyExperiment: Bioclipse ScriptingLanguage



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



Where next?

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

ProteochemometricsKnowledge discoveryData set aggregationAutomated model validation



The Details

http://www.citeulike.org/user/

egonw/tag/papers

http:

//chem-bla-ics.blogspot.com

http://egonw.github.com

waveto:

[email protected]


http://www.citeulike.org/user/egonw/tag/papers

http://www.citeulike.org/user/egonw/tag/papers

http://chem-bla-ics.blogspot.com

http://chem-bla-ics.blogspot.com

http://egonw.github.com

waveto:[email protected]

waveto:[email protected]


Linking Open Drug Data to Cheminformatics and Proteochemometrics

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