open knowledge: reproducibility in cheminformatics with open data, open source, and open standards

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Open Knowledge: Reproducibility in Cheminformatics 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

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My presentation at the "Open Drug Discovery and Open Notebook Science" session at the GDCh-Wissenschaftsforum Chemie 2009 in Frankfurt.

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Page 1: 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

Page 2: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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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

Page 3: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Reliable Knowledge: Trust

How to build Trusttrack record

2009-08-31 Bioclipse & Proteochemometric Group - 3 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 4: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Knowledge: Trust

How to build Trusttrack recordtransparency: citation

2009-08-31 Bioclipse & Proteochemometric Group - 4 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 5: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Knowledge: Trust

How to build Trusttrack recordtransparency: citationreproducibility: details

2009-08-31 Bioclipse & Proteochemometric Group - 5 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 6: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Knowledge: Trust

How to build Trusttrack recordtransparency: citationreproducibility: details

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

2009-08-31 Bioclipse & Proteochemometric Group - 6 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 7: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Knowledge Representation...

What are theorganic normalconditions?

2009-08-31 Bioclipse & Proteochemometric Group - 7 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 8: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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The Problem: Reproducibility...

Where reproducibility isseverely hampered:

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

2009-08-31 Bioclipse & Proteochemometric Group - 8 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 9: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Solutions...

Openesslicense that allowsmodification andredistributionhiding behind publicdomain is not helpful

Semantic Webbe explicit in what youmeanboth in facts and inalgorithms

2009-08-31 Bioclipse & Proteochemometric Group - 9 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 10: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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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

2009-08-31 Bioclipse & Proteochemometric Group - 10 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 11: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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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/

2009-08-31 Bioclipse & Proteochemometric Group - 11 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 12: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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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

2009-08-31 Bioclipse & Proteochemometric Group - 12 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 13: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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CDK: an Open Project

Featuresopen mailinglist and bugtrackeropen source repositoryrelease soon, release often

Offer Reviewsenior developers reviewpatches

2009-08-31 Bioclipse & Proteochemometric Group - 13 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 14: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Bioclipse

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

2009-08-31 Bioclipse & Proteochemometric Group - 14 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 15: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Integration

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

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

2009-08-31 Bioclipse & Proteochemometric Group - 15 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 16: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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MyExperiment: Bioclipse ScriptingLanguage

2009-08-31 Bioclipse & Proteochemometric Group - 16 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 17: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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XMPP

XMPPJabberprotocolAlternative toHTTPXML-based:improvedsemantics

FeaturesAsychronousXML-based:improvedsemantics

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

2009-08-31 Bioclipse & Proteochemometric Group - 17 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 18: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Resource Description Framework

Facts as Triplessubjectpredictate (relation)object

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

2009-08-31 Bioclipse & Proteochemometric Group - 18 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 19: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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OpenMolecules RDF

http://rdf.openmolecules.net/

2009-08-31 Bioclipse & Proteochemometric Group - 19 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 20: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Blue Obelisk

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

2009-08-31 Bioclipse & Proteochemometric Group - 20 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 21: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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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

2009-08-31 Bioclipse & Proteochemometric Group - 21 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 22: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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Mixing Data?

License IncompatibilityAsk about the copyrightholders intention!

Use Open Standard InterfacesResource DescriptionFramework

2009-08-31 Bioclipse & Proteochemometric Group - 22 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 23: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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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

2009-08-31 Bioclipse & Proteochemometric Group - 23 - Egon Willighagen | chem-bla-ics.blogspot.com

Page 24: Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source, and Open Standards

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The Details

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

egonw/tag/papers

http:

//chem-bla-ics.blogspot.com

mailto:

[email protected]

2009-08-31 Bioclipse & Proteochemometric Group - 24 - Egon Willighagen | chem-bla-ics.blogspot.com