Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.
Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.
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DOI：
10.1093/bioinformatics/btw731
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发表时间：
2017-04-01
期刊：
影响因子：
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通讯作者：
Auffray C
中科院分区：
文献类型：
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作者：
Balaur I;Mazein A;Saqi M;Lysenko A;Rawlings CJ;Auffray C
这项工作的目标是提供一个计算框架，用于探索Recon2人体代谢重建模型的数据。使用Neo4j图形数据库技术开发了高级用户访问功能，本文描述了关键功能，如网络数据的有效管理，解决特定任务的网络查询示例，以及查询结果如何转换回系统生物学标记语言（SBML）标准格式。基于Neo4j的代谢框架有助于探索高度连接和全面的人类代谢数据，并识别感兴趣的代谢子网络。开发了一个基于Java的解析器组件，用于将查询结果（JSON格式）转换为SBML和SIF格式，以促进进一步的结果探索、增强或网络共享。基于Neo4j的代谢框架可从https://diseaseknowledgebase.etriks.org/metabolic/browser/免费获得。为这项工作开发的java代码文件可以从以下网址获得：https://github.com/ibalaur/MetabolicFramework。 补充数据可在Bioinformatics在线获得。
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. 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. Supplementary data are available at Bioinformatics online.