Software and demos for Cheminformatics Open Source meeting at EBI

#wwmm #quixotechem #blueobelisk

I do not present software through Powerpoint but through living links and demos. These all worked when they were entered here. All demos decay…


We ( have built a wide-ranging series of components to support Open chemistry. They are mainly based on Chemical Markup Language (CML)

  • Recent presentation from Sam Adams at ACS covers much of the ground (especially Chempound)


Multicomponent demos include:

  • Searching Chempound repository for a Chem4Word document and using OPSIN to translate name2structure
  • Running Lensfield on commandline to parse directory of compchem output into CML

All demos and software ore Open (Artistic, GPL , CC-BY, PDDL, CC0)


(CML) infrastructure and include:

OSCAR4, a modular system for textmining;


OPSIN, a name2structure converter (Daniel Lowe et al.);

ChemicalTagger, a natural language system for chemistry;

JUMBOConverters which process collections of legacy material (including computational logfiles) into semantic form;

Chempound, a semantic RDF repository for any chemistry;

Crystaleye, an automatic aggregator of crystal structures and publications;

Lensfield, a make facility for data.

Metaprint, an Open source tool for predicting sites of metabolism

JNI-InChI (Sam Adams)

See also:

Much of this is being formally written up for a special issue of J. Cheminformatics (BMC).

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