Fig. 1

Workflow of STON software. This figure shows the workflow of the STON framework: an SBGN-ML file is provided as the input to the framework. It is parsed by STON and converted into a graph representation using the mapping rules described in the Additional file 1. The resulting data is then stored in a local directory as nodes, relationships and properties. Neo4j relies on this repository and, if run as a web server instance, offers a visualization of the data. The repository can be queried for biological entities, relations in the network, and similar nodes across networks, as described in the “Results” section. The example is the IFNG receptor, a biological complex composed of four subunits: IFNGR1 and IFNGR2 that are dimerised, and JAK1 and JAK2 that are macromolecules. In Neo4J, all entities are connected to the complex node with the relationship belongs_to_complex