StonPy：一个在图数据库中解析和查询 SBGN 图集合的工具。

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

机构信息

Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.

Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Tokyo 169-8555, Japan.

出版信息

Bioinformatics. 2023 Mar 1;39(3). doi: 10.1093/bioinformatics/btad100.

DOI:10.1093/bioinformatics/btad100

PMID:36897014

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10017094/

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.

摘要

系统生物学图形符号 (SBGN) 已成为分子图谱图形表示的事实上的标准。快速方便地访问大型图谱集合的内容对于对这些资源进行语义或基于图的分析是必要的。为此，我们提出了 StonPy，这是一种用于在 Neo4j 图形数据库中存储和查询 SBGN 图谱的新工具。StonPy 特别包括一个数据模型，该模型考虑了所有三种 SBGN 语言，以及一个补全模块，可从查询结果自动构建有效的 SBGN 图谱。StonPy 被构建为一个可以集成到其他软件中的库，并提供一个命令行接口，允许用户轻松执行所有操作。