MINERVA-a platform for visualization and curation of molecular interaction networks
MINERVA-a platform for visualization and curation of molecular interaction networks
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DOI：
10.1038/npjsba.2016.20
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发表时间：
2016-01-01
影响因子：
4
通讯作者：
Schneider, Reinhard
中科院分区：
文献类型：
--
作者：
Gawron, Piotr;Ostaszewski, Marek;Schneider, Reinhard
我们对各种分子机制的了解越来越多，并且变得越来越结构化和易于理解。不同的分子相互作用存储库和可用文献可以构建有针对性的高质量分子相互作用网络。为了促进系统生物学环境的发展，需要用于管理和探索此类网络的新工具。特别是，可视化、注释和数据交叉链接的解决方案将促进网络编码知识在生物医学研究中的使用。为此，我们开发了 MINERVA（分子相互作用网络可视化）平台，这是一个独立的网络服务，支持以系统生物学图形符号 (SBGN) 兼容的格式对分子相互作用网络进行管理、注释和可视化。 MINERVA 提供自动内容注释和验证，以改进质量控制。最终用户可以探索托管网络并与之交互，并向内容管理者提供直接反馈。 MINERVA 能够在可视化网络上绘制药物靶标或叠加实验数据。广泛的导出功能可以将可视化网络区域下载为符合 SBGN 的模型，从而有效地重用托管网络。该软件可在 Affero GPL 3.0 下作为虚拟机快照、Debian 软件包和 Docker 实例在 http://r3lab.uni.lu/web/minerva-website/ 上使用。我们相信 MINERVA 对系统生物学界做出了重要贡献，因为它的架构能够建立本地或全球可访问的面向 SBGN 的分子相互作用网络存储库。其功能允许叠加多个信息层，促进内容探索和数据解释。此外，MINERVA的注释和验证工作流程提高了网络管理的效率，使生命科学研究人员能够更好地参与生物医学知识库的开发和使用。
Our growing knowledge about various molecular mechanisms is becoming increasingly more structured and accessible. Different repositories of molecular interactions and available literature enable construction of focused and high-quality molecular interaction networks. Novel tools for curation and exploration of such networks are needed, in order to foster the development of a systems biology environment. In particular, solutions for visualization, annotation and data cross-linking will facilitate usage of network-encoded knowledge in biomedical research. To this end we developed the MINERVA (Molecular Interaction NEtwoRks VisuAlization) platform, a standalone webservice supporting curation, annotation and visualization of molecular interaction networks in Systems Biology Graphical Notation (SBGN)-compliant format. MINERVA provides automated content annotation and verification for improved quality control. The end users can explore and interact with hosted networks, and provide direct feedback to content curators. MINERVA enables mapping drug targets or overlaying experimental data on the visualized networks. Extensive export functions enable downloading areas of the visualized networks as SBGN-compliant models for efficient reuse of hosted networks. The software is available under Affero GPL 3.0 as a Virtual Machine snapshot, Debian package and Docker instance at http://r3lab.uni.lu/web/minerva-website/. We believe that MINERVA is an important contribution to systems biology community, as its architecture enables set-up of locally or globally accessible SBGN-oriented repositories of molecular interaction networks. Its functionalities allow overlay of multiple information layers, facilitating exploration of content and interpretation of data. Moreover, annotation and verification workflows of MINERVA improve the efficiency of curation of networks, allowing life-science researchers to better engage in development and use of biomedical knowledge repositories.