Opentox Virtual Seminar: Bioclipse - Life Science Application and Ontology Development in Cheminformatics and Bioinformatics

The CDK, Bioclipse, and RDF

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

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

Uppsala University

2010-04-01

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

Problem

BuildingBlocks

Solution

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Who am I?

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

egonw/tag/papers

http:

//chem-bla-ics.blogspot.com

http://egonw.github.com

waveto:

[email protected]

2010-04-01 Bioclipse & Proteochemometric Group - 2 - Egon Willighagen | chem-bla-ics.blogspot.com

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]

chem-bla-ics.blogspot.com

Problem

BuildingBlocks

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The Problem...

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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The Setting...

1998: Organicchemistry...beatiful science!But ... why, how,what, ...

PJJA Buijnsters et al., Eur.J.Org.Chem, 2002, 1397–1406



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Knowledge Representation...

What are theorganic normalconditions?



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The Problem: Reproducibility...

Where reproducibility isseverely hampered:

recalculate basic atom andbond propertiesaccess to QSAR/QSPRdatawell-defined algorithmspublications destroyinformation



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Solutions...

Openesslicense that allowsmodification andredistributionhiding behind publicdomain is not helpful

Semantic Webbe explicit in what youmeanboth in facts and inalgorithms



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Reproducibility needs ODOSOS

Open DataNo Intellectual Monopoly

Open Sourcealgorithms are compleximplementations even morestrong interaction with representation

Open StandardsSemantic Webformatsunique identifiers

http: // en. wikipedia. org/ wiki/ Glyn_ Moody


http://en.wikipedia.org/wiki/Glyn_Moody


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Jmol

Started in 1997 byDan Gezelter(Notre Dame)Leaders: BradlySmith, me, MiguelHoward, BobHanson

E.L. Willighagen, M. Howard, Nature Precedings, 2005http: // www. jmol. org/


http://www.jmol.org/


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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 2003: 75+ times cited in 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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CDK: an Open Project

Featuresopen mailinglist and bugtrackeropen source repositoryrelease soon, release often

Offer Reviewsenior developers reviewpatches



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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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Resource Description Framework

Facts as Triplessubjectpredictate (relation)object

Exampleswp:Benzenechem:hasSMILES"c1ccccc1"wp:Benzene owl:sameAschemspider:123



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OpenMolecules RDF: dereferenceable URI

http://rdf.openmolecules.net/




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OpenMolecules RDF: linked data





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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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Names 2 Graphs 2 Numbers...



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ChEMBL / QSAR



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RDF graph visualization



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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



Health & Medicine

Opentox Virtual Seminar: Bioclipse - Life Science Application and Ontology Development in Cheminformatics and Bioinformatics