From the website:
Bio4j is a bioinformatics graph based DB including most data available in UniProt (SwissProt + Trembl), Gene Ontology (GO) and UniRef (50,90,100).
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. On the contrary, traditional relational databases must flatten the data they represent into tables, creating “artificial” ids in order to connect the different tuples; which can in some cases eventually lead to domain models that have almost nothing to do with the actual structure of data.
I am particularly interested in incorporate you own data feature:
New data sources and features will be added from time to time and what it’s more important, the Java API allows you to easily incorporate your own data to Bio4j so you can make the best out of it.