Chemical Interoperability

Egon Willighagen

BiGCaT – Dept of Bioinformatics

2012-02-17, Utrecht

Interoperability in Chemistry

• = Communication, meaning

• Why?–Reproducibility–Understanding molecular properties

• Interoperability Needs–Open Data, Open Standards, Open Source

What's that Open fetish?

• Gives–Collaboration. Credit. Ownership.–Sustainability.

• Trough rights–Redistribution (under same rights)–Modification (not with Open Standards)

The Blue Obelisk Movement

R. Guha et al. J. Chem. Inf. Mod. 2006 N. O'Boyle et al. J. Cheminf. 2011

1. Open Standards

• Allows:–Software to talk to each other

• For:–Well-defined formats–Concepts (aromaticity!)–Practices (licenses, peer review, ...)

CML: Exchange of Chemical Structures

P. Murray-Rust et al, J. Chem. Inf. Comput. Sci., 1999E.L. Willighagen, Internet J. Chem., 2000

CML in RSS news feeds

P. Murray-Rust et al., J. Chem. Inf. Comput. Sci, 2004

Resource Description Framework

• Family of W3C technologies–RDF / RDFS: basic framework–Serialization formats

• RDF/XML, Turtle, RDFa, RDF/JSON

–OWL: ontologies (BioPortal, OLS, …)–SPARQL

SemanticWeb

IUPAC International Chemical Identifier

N. Day. InChI FAQ, http://wwmm.ch.cam.ac.uk/inchifaq/

2. Open Data

• What is the average C=N bond length?–Bioinformatics: force fields

• What is the LogP of aspirin?–Drug discovery

• What metabolite is that?–Metabolomics

Linked Open Drug Data

M. Samwald et al., J. Cheminf, 2011

Blue Obelisk Data Repository

● Which two tools calculate the same molecular weight?

● Isotope abundancies and weights!● IUPAC reports

R. Guha et al. J. Chem. Inf. Mod. 2006

3. Open Source

• What is aromaticity?

Chemistry Development Kit

• Cheminformatics–Aromaticity– ...

• Many derived tools–Taverna, KNIME, Bioclipse, Cinfony, ...

C. Steinbeck et al. J. Chem. Inf. Mod. 2003C. Steinbeck et al. Curr. Pharm. Des. 2006

Scripting ...

O. Spjuth et al. BMC Bioinf. 2009T. Kuhn et al. BMC Bioinf. 2010

Predictive Toxicology I

O. Spjuth et al. J. Chem. Inf. Mod. 2011E.L. Willighagen et al. BMC Research Notes. 2011

Predictive Toxicology II

E.L. Willighagen et al. J. Biomed Sem. 2011

Conclusions

• Interoperability via ODOSOS–Open Data–Open Standards–Open Source

Thanx / More info

• Blue Obelisk movement• CDK developers (Miguel!)

• http://scholar.google.com/citations?user=u8SjMZ0AAAAJ

• http://chem-bla-ics.blogspot.com/