StonPy: a tool to parse and query collections of SBGN maps in a graph database.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 03 2023
01 03 2023
Historique:
received:
23
08
2022
revised:
14
01
2023
pubmed:
11
3
2023
medline:
21
3
2023
entrez:
10
3
2023
Statut:
ppublish
Résumé
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. 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 data are available at Bioinformatics online.
Identifiants
pubmed: 36897014
pii: 7075543
doi: 10.1093/bioinformatics/btad100
pmc: PMC10017094
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : P41 GM103504
Pays : United States
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
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