BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. 

BioJava - Java Framework for Processing Biological Data

Bio4j is a bioinformatics graph based DB including most data available in Uniprot KB (SwissProt + Trembl), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI Taxonomy, and Expasy Enzyme DB.
Bio4j provides a completely new and powerful framework for protein related information querying and management. Since it relies on a  high-performance graph engine, data is stored in a way that semantically represents its own structure. 

Bio4j - Bioinformatics Graph based DB

A powerful open source data warehouse system. InterMine allows users to integrate diverse data sources with a minimum of effort, providing powerful web-services and an elegant web-application with minimal configuration. InterMine powers some of the largest data-warehouses in the life sciences.

Intermine - A powerful open source data warehouse system

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BioJava - Java Framework for Processing Biological Data

Bio4j - Bioinformatics Graph based DB

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BioJava - Java Framework for Processing Biological Data

Bio4j - Bioinformatics Graph based DB

Intermine - A powerful open source data warehouse system

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