Applications of the InChI in cheminformatics with the CDK and Bioclipse.

O. Spjuth*, A. von Berg, S. Adams, E.L. Willighagen

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Web of Science)


Background The InChI algorithms are written in C++ and not available as library.Integration into software written in Java therefore requires a between C and Java libraries,provided by the Java Native Interface (JNI) technology.Results We here describe how the InChI library is used in the Bioclipse workbench and the Chemistry Development Kit (CDK) library. To make this possible, a JNI bridge to the InChI library was JNI-InChI, allowing Java software to access the InChI algorithms. By bridge, the CDK project packages the InChI binaries in a module and access from Java using the CDK API. The Bioclipse project packages and InChI as a dynamic OSGi bundle that can easily be used by any OSGi- software, in addition to the regular Java Archive and Maven bundles. itself uses the InChI as a key component and calculates it on the fly visualizing and editing chemical structures. We demonstrate the utility with various applications in CDK and Bioclipse, such as decision support chemical liability assessment, tautomer generation, and for knowledge using a linked data approach.Conclusions These results show that the library can be used in a variety of Java library dependency solutions, functionality easily accessible by Java software, such as in the CDK. applications show various ways the InChI has been used in Bioclipse, to its functionality.
Original languageEnglish
Article number14
Number of pages7
JournalJournal of Cheminformatics
Issue number1
Publication statusPublished - 13 Mar 2013


  • InChI
  • InChIKey
  • Chemical structures
  • JNI-InChI
  • The Chemistry Development Kit
  • OSGi
  • Bioclipse
  • Decision support
  • Linked data
  • Tautomers
  • Databases
  • Semantic web
  • WEB

Cite this