Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

Open Knowledge: Reproducibility inCheminformatics with Open Data, Open

Source and Open Standards

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

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

Uppsala University

2009-08-31

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

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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

2009-08-31 Bioclipse & Proteochemometric Group - 2 - Egon Willighagen | chem-bla-ics.blogspot.com

chem-bla-ics.blogspot.com

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Reliable Knowledge: Trust

How to build Trusttrack record



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Knowledge: Trust

How to build Trusttrack recordtransparency: citation



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Knowledge: Trust

How to build Trusttrack recordtransparency: citationreproducibility: details



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Knowledge: Trust

How to build Trusttrack recordtransparency: citationreproducibility: details

Open {Data|Standards|Source|. . . }



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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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MyExperiment: Bioclipse ScriptingLanguage



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XMPP

XMPPJabberprotocolAlternative toHTTPXML-based:improvedsemantics

FeaturesAsychronousXML-based:improvedsemantics

J. Wagener et al., BMC Bioinformatics, 2009, in production



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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

http://rdf.openmolecules.net/


http://rdf.openmolecules.net/


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Blue Obelisk

R Guha et al., J.Chem.Inf.Model.,2006



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Which License?

ChoiceGPL v2 or v3, LGPL v2 orv3, Apache, BSD, MIT, ...FDL, CC0, PDDLImportant: redistribution,modification

Bad Practisenot explicitly stating yourintentionsPublic Domain



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Mixing Data?

License IncompatibilityAsk about the copyrightholders intention!

Use Open Standard InterfacesResource DescriptionFramework



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Conclusions

No Intellectual Monopoly AcchievedJmol, CDK, JChemPaint, Bioclipse

• A huge success!Open Data in chemistry is still way behind

• Open Access trap• Public Domain trap

Semantics is showing up• in RDF• in Publishing



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The Details

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

egonw/tag/papers

http:

//chem-bla-ics.blogspot.com

mailto:

[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

mailto:[email protected]

mailto:[email protected]


Technology

Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards