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. 2023 Jun 22;3:1197310. doi: 10.3389/fbinf.2023.1197310

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Copyright © 2023 Mazein, Acencio, Balaur, Rougny, Welter, Niarakis, Ramirez Ardila, Dogrusoz, Gawron, Satagopam, Gu, Kremer, Schneider and Ostaszewski.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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An SBGN map and an excerpt of its corresponding Neo4j graph built using the StonPy software. SBGN nodes (e.g., proteins, states variables) are modelled using Neo4j nodes, while SBGN arcs (e.g., catalyses, production arcs) and relationships between concepts are modelled using Neo4j relationships (edges). Neo4j nodes are labelled (e.g., “Glyph”, “Macromolecule”) and may contain key-value pairs (e.g., the pair “label”/“MAPK3”). Additionally, annotations are stored in a structured form that can be easily queried. In the complete model (not shown), SBGN arcs are additionally modelled using Neo4j nodes, as they may contain SBGN nodes themselves.