ArticleJournal of cheminformatics2013
Applications of the InChI in cheminformatics with the CDK and Bioclipse.
Article in Journal of cheminformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Quantum Chemistry Calculations for Metabolomics.Chemical reviews · 2021Review
- The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.Journal of cheminformatics · 2017Article
- The metabolome 18 years on: a concept comes of age.Metabolomics : Official journal of the Metabolomic Society · 2016Review
- Many InChIs and quite some feat.Journal of computer-aided molecular design · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsWe 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.
conclusionsThese 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.
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Registered trials
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