Available Software

BioGraphDB: A Bioinformatics GraphDB based on Integration of Publicly Available Databases

BioGraphDB is an integrated database that collects and links heterogeneous bioinformatics resources. It is implemented using a NoSQL graph database built upon the OrientDB platform. Graph databases allow, in fact, a greater scalability and queries efficiency with regards to the size of data, rather than traditional SQL database. Each component database has been downloaded from its original site and it has been processed using customized Extract-Transformer-Loader (ETL) modules, in order to be assembled into a graph architecture. Each biological entity and its properties have been mapped respectively into a vertex and its attributes, and each relationship between two biological entities has been mapped into an edge. The whole assembled graph can be traversed using proper query languages, such as Gremlin. Each graph traversal represents a set of queries that are enough in order to solve several bioinformatics scenarios.