Applications of the InChI in cheminformatics with the CDK and Bioclipse

Applications of the InChI in cheminformatics with the CDK and Bioclipse
Authored by:
Ola Spjuth
Arvid Berg
Samuel Adams
Egon L. Willighagen

Abstract

Background

The InChI algorithms are written in C++ and not available as Java library. Integration into software written in Java therefore requires a bridge 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) cheminformatics library. To make this possible, a JNI bridge to the InChI library was developed, JNI-InChI, allowing Java software to access the InChI algorithms. By using this bridge, the CDK project packages the InChI binaries in a module and offers easy access from Java using the CDK API. The Bioclipse project packages and offers InChI as a dynamic OSGi bundle that can easily be used by any OSGi-compliant software, in addition to the regular Java Archive and Maven bundles. Bioclipse itself uses the InChI as a key component and calculates it on the fly when visualizing and editing chemical structures. We demonstrate the utility of InChI with various applications in CDK and Bioclipse, such as decision support for chemical liability assessment, tautomer generation, and for knowledge aggregation using a linked data approach.

Conclusions

These results show that the InChI library can be used in a variety of Java library dependency solutions, making the functionality easily accessible by Java software, such as in the CDK. The applications show various ways the InChI has been used in Bioclipse, to enrich its functionality.

Keywords:

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

Information
Content Type OER
Uploaded By Andrew Cornell
DOI https://doi.org/10.1186/1758-2946-5-14
Content Link https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-5-14
License Open Access
Content Status publish
Number of Comments No Comments
Date Published March 13, 2013
Content Tags Algorithm, Application, Audience, Bioinformatics, Cheminformatics, Content type, Curricular Material, Data Extraction, English, File Type, Graduate, InChI Algorithm and Description, InChI Application, Language, PDF, Publication, Researcher, Script, Software, Toolkits, Undergraduate, ePub