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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
The main home page of the CDK is now at: http://cdk.github.io
OBOES (Open Biomedical Ontology-Based Enrichment and Search) is an information-theory-based platform that embeds new integrative methods allowing biologists to evaluate new hypotheses.