STON: exploring biological pathways using the SBGN standard and graph databases.

ABSTRACT:

Background

When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks.

Results

We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database.

Conclusion

STON exploits the power of graph databases to store and query complex biological pathways. This advances the possibility of: i) identifying su

SUBMITTER: Toure V 

PROVIDER: S-EPMC5139139 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature