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

Adrien Rougny; Irina Balaur; Augustin Luna; Alexander Mazein

doi:10.1093/bioinformatics/btad100

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

Adrien Rougny^*, Irina Balaur, Augustin Luna, Alexander Mazein

^*Corresponding author for this work

Research output: Contribution to journal › Article › Research › peer-review

3 Citations (Scopus)

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.

Original language	English
Article number	btad100
Journal	Bioinformatics
Volume	39
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btad100
Publication status	Published - 1 Mar 2023
Externally published	Yes

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title = "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.",

author = "Adrien Rougny and Irina Balaur and Augustin Luna and Alexander Mazein",

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AU - Luna, Augustin

AU - Mazein, Alexander

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AB - 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.

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

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