StonPy: a tool to parse and query collections of SBGN maps in a graph database

Abstract

Summary: The systems biology graphical notation (SBGN) has become the de facto standard for the graphical representation of molecular maps. Having rapid and easy access to the content of large collections of maps is necessary to perform semantic or graph-based analysis of these resources. To this end, we propose StonPy, a new tool to store and query SBGN maps in a Neo4j graph database. StonPy notably includes a data model that takes into account all three SBGN languages and a completion module to automatically build valid SBGN maps from query results. StonPy is built as a library that can be integrated into other software and offers a command-line interface that allows users to easily perform all operations.

Availability and implementation: StonPy is implemented in Python 3 under a GPLv3 license. Its code and complete documentation are freely available from https://github.com/adrienrougny/stonpy.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Overview of StonPy’s functionalities. An example of an input SBGN PD map is shown on the left. The corresponding Neo4j graph, built using StonPy, is shown on the right. All SBGN glyphs and arcs are modeled using Neo4j nodes; relationships between SBGN glyphs and sub-glyphs or complex attributes are modeled using Neo4j relationships. SBGN arcs are optionally modeled using additional Neo4j relationships (CATALYZES, HAS_REACTANT, and HAS_PRODUCT relationships) that mimic the structure of the SBGN map and facilitate writing queries on the represented biological concepts. For each Neo4j node, either one of its labels or one of its attributes is shown; for each label, its type is shown. Examples of labels and attributes are shown for some Neo4j nodes in the boxes on the right. Consumption (Cons) and Production (Prod) have been shortened for visualization