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

The Setting...
Problem
Solution
Results
Discussions
1998: Organic
Conclusion chemistry...
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

Reliable Knowledge: Trust
Problem
Solution
Results
Discussions
How to build Trust
Conclusion
track record
2009-08-31 Bioclipse & Proteochemometric Group -3- Egon Willighagen | chem-bla-ics.blogspot.com

Knowledge: Trust
Problem
Solution
Results
Discussions
How to build Trust
Conclusion track record
transparency: citation
2009-08-31 Bioclipse & Proteochemometric Group -4- Egon Willighagen | chem-bla-ics.blogspot.com

Knowledge: Trust
Problem
Solution
Results How to build Trust
Discussions
track record
Conclusion
transparency: citation
reproducibility: details
2009-08-31 Bioclipse & Proteochemometric Group -5- Egon Willighagen | chem-bla-ics.blogspot.com

Knowledge: Trust
Problem
Solution How to build Trust
Results track record
Discussions
transparency: citation
Conclusion
reproducibility: details
Open {Data|Standards|Source|. . . }
2009-08-31 Bioclipse & Proteochemometric Group -6- Egon Willighagen | chem-bla-ics.blogspot.com

Knowledge Representation...
Problem
Solution
Results
Discussions
Conclusion
What are the
organic normal
conditions?
2009-08-31 Bioclipse & Proteochemometric Group -7- Egon Willighagen | chem-bla-ics.blogspot.com

The Problem: Reproducibility...
Problem
Where reproducibility is
Solution
severely hampered:
Results
Discussions
recalculate basic atom and
Conclusion bond properties
access to QSAR/QSPR
data
well-defined algorithms
publications destroy
information
2009-08-31 Bioclipse & Proteochemometric Group -8- Egon Willighagen | chem-bla-ics.blogspot.com

Solutions...
Openess
Problem
license that allows
Solution
modification and
Results
redistribution
Discussions
Conclusion
hiding behind public
domain is not helpful
Semantic Web
be explicit in what you
mean
both in facts and in
algorithms
2009-08-31 Bioclipse & Proteochemometric Group -9- Egon Willighagen | chem-bla-ics.blogspot.com

Reproducibility needs ODOSOS
Open Data
Problem No Intellectual Monopoly
Solution Open Source
Results
algorithms are complex
Discussions
Conclusion
implementations even more
strong interaction with representation
Open Standards
Semantic Web
formats
unique identifiers
http: // en. wikipedia. org/ wiki/ Glyn_ Moody
2009-08-31 Bioclipse & Proteochemometric Group - 10 - Egon Willighagen | chem-bla-ics.blogspot.com

Jmol
Problem
Solution Started in 1997 by
Results Dan Gezelter
Discussions (Notre Dame)
Conclusion
Leaders: Bradly
Smith, me, Miguel
Howard, Bob
Hanson
E.L. Willighagen, M. Howard, Nature Precedings, 2005
http: // www. jmol. org/
2009-08-31 Bioclipse & Proteochemometric Group - 11 - Egon Willighagen | chem-bla-ics.blogspot.com

The Chemistry Development Kit
A Family of Projects
CDK-Taverna (chemoinformatics workflows)
Problem
Solution
JChemPaint (semantic 2D editor)
Results ChemoJava (GPL-ed extension)
Discussions Goals
Conclusion
library of cheminformatics algorithms
educational
Usage
CDK 2003: 75+ times cited in literature
Bioclipse, KNIME, Jumbo (CML), AMBIT, ...
C. Steinbeck et al., J.Chem.Inf.Comput.Sci, 2003
C. Steinbeck et al., Curr.Pharm.Design, 2006
2009-08-31 Bioclipse & Proteochemometric Group - 12 - Egon Willighagen | chem-bla-ics.blogspot.com

CDK: an Open Project
Problem
Features
Solution
open mailinglist and bug
Results
Discussions
tracker
Conclusion open source repository
release soon, release often
Offer Review
senior developers review
patches
2009-08-31 Bioclipse & Proteochemometric Group - 13 - Egon Willighagen | chem-bla-ics.blogspot.com

Bioclipse
Problem
Solution
Results
Discussions
Conclusion
O. Spjuth et al., BMC Bioinformatics 2007, 8:59
2009-08-31 Bioclipse & Proteochemometric Group - 14 - Egon Willighagen | chem-bla-ics.blogspot.com

Integration
Services
databases: PubChem
Problem
Solution
web services
Results Google Spreadsheets
Discussions
MyExperiment.org: Bioclipse
Conclusion
Scripting Language
Twitter, ...
journals, ...
Techniques
SOAP, REST, XMPP, . . .
Resource Description Framework
dedicated APIs
2009-08-31 Bioclipse & Proteochemometric Group - 15 - Egon Willighagen | chem-bla-ics.blogspot.com

MyExperiment: Bioclipse Scripting
Language
Problem
Solution
Results
Discussions
Conclusion
2009-08-31 Bioclipse & Proteochemometric Group - 16 - Egon Willighagen | chem-bla-ics.blogspot.com

XMPP
XMPP
Jabber
Problem protocol
Solution
Alternative to
Results
HTTP
Discussions
Conclusion
XML-based:
improved
semantics
Features
Asychronous
XML-based:
improved
semantics
J. Wagener et al., BMC Bioinformatics, 2009, in production
2009-08-31 Bioclipse & Proteochemometric Group - 17 - Egon Willighagen | chem-bla-ics.blogspot.com

Resource Description Framework
Problem
Facts as Triples
Solution subject
Results
predictate (relation)
Discussions
Conclusion
object
Examples
wp:Benzene
chem:hasSMILES
"c1ccccc1"
wp:Benzene owl:sameAs
chemspider:123
2009-08-31 Bioclipse & Proteochemometric Group - 18 - Egon Willighagen | chem-bla-ics.blogspot.com

OpenMolecules RDF
Problem
Solution
Results
Discussions
Conclusion
http://rdf.openmolecules.net/
2009-08-31 Bioclipse & Proteochemometric Group - 19 - Egon Willighagen | chem-bla-ics.blogspot.com

Blue Obelisk
Problem
Solution
Results
Discussions
Conclusion
R Guha et al., J.Chem.Inf.Model.,
2006
2009-08-31 Bioclipse & Proteochemometric Group - 20 - Egon Willighagen | chem-bla-ics.blogspot.com

Which License?
Choice
Problem
Solution
GPL v2 or v3, LGPL v2 or
Results v3, Apache, BSD, MIT, ...
Discussions FDL, CC0, PDDL
Conclusion
Important: redistribution,
modification
Bad Practise
not explicitly stating your
intentions
Public Domain
2009-08-31 Bioclipse & Proteochemometric Group - 21 - Egon Willighagen | chem-bla-ics.blogspot.com

Mixing Data?
Problem
Solution
License Incompatibility
Results
Discussions
Ask about the copyright
Conclusion holders intention!
Use Open Standard Interfaces
Resource Description
Framework
2009-08-31 Bioclipse & Proteochemometric Group - 22 - Egon Willighagen | chem-bla-ics.blogspot.com

Conclusions
Problem
No Intellectual Monopoly Acchieved
Solution
Jmol, CDK, JChemPaint, Bioclipse
Results
• A huge success!
Discussions
Conclusion 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

The Details
Problem
Solution
Results
http://www.citeulike.org/user/
Discussions
egonw/tag/papers
Conclusion
http:
//chem-bla-ics.blogspot.com
mailto:
egon.willighagen@farmbio.uu.se
2009-08-31 Bioclipse & Proteochemometric Group - 24 - Egon Willighagen | chem-bla-ics.blogspot.com