Databases, Factual; Language; Documentation; Systems Biology/methods; Software; Statistics and Probability; Biochemistry; Molecular Biology; Computer Science Applications; Computational Theory and Mathematics; Computational Mathematics
Abstract :
[en] [en] 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.
Disciplines :
Biotechnology
Author, co-author :
Rougny, Adrien ; 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
BALAUR, Irina-Afrodita ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Luna, Augustin; Department of Systems Biology, Harvard Medical School, Boston, MA, USA ; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
MAZEIN, Alexander ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
External co-authors :
yes
Language :
English
Title :
StonPy: a tool to parse and query collections of SBGN maps in a graph database.
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