Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Apr 1;33(7):1096-1098.
doi: 10.1093/bioinformatics/btw731.

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

Irina Balaur  1 , Alexander Mazein  1 , Mansoor Saqi  1 , Artem Lysenko  2 , Christopher J Rawlings  2 , Charles Auffray  1
Affiliations

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

Irina Balaur et al. Bioinformatics. .

Abstract

Summary: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing.

Availability and implementation: The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework .

Contact: ibalaur@eisbm.org.

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Visualization using CellDesigner (Funahashi et al., 2008) for the arachidonic acid metabolic network identified based on Cypher query 1 (Supplementary file S4)
See this image and copyright information in PMC

References

    1. Dräger A. et al. (2011) JSBML: a flexible Java library for working with SBML. Bioinformatics, 2727, 2167–2168. - PMC - PubMed
    1. Funahashi A. et al. (2008) CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc. IEEE, 9696, 1254–1265.
    1. Hucka M. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 1919, 524–531. - PubMed
    1. König M. et al. (2012) CySBML: a Cytoscape plugin for SBML. Bioinformatics, 2828, 2402–2403. - PubMed
    1. Lysenko A. et al. (2016) Representing and querying disease networks using graph databases. BioData Min., 99, 23. - PMC - PubMed