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

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