The Network Data Exchange - a Network Commons for Biologists

网络数据交换--生物学家的网络共享 项目摘要 生物网络的知识对于分析大型生物医学数据集至关重要，包括 在肿瘤内和肿瘤间观察到的分子异质性的解释。NDEx，网络数据交换 （ndexbio.org），是一个在线共享，科学家发现，共享和公开分发生物网络。 在癌症研究计划信息技术（ITCR U24 CA184427）的资助下， 我们创建了NDEx开放源代码数据库平台，沿着推出了其公共网站和查询系统。此外，本发明还 我们实现了与Python和R数据科学平台的互操作性，并将NDEx无缝构建到 Cytoscape网络分析和可视化生态系统。NDEx目前为大量用户提供服务， 网络内容，约有3285个账户链接到> 180，000个网络，其中约有6500个 都是公开的NDEx是Springer Nature上发表文章的经批准的网络存储库 和公共科学图书馆（PLoS）系列期刊。 我们正在为NDEx项目申请持续的ITCR资金，以维护、扩展和增强NDEx 系统，通过以下五个具体目标满足生物医学研究界不断变化的需求： 1.维护和扩展NDEx及其服务，以支持庞大且不断增长的用户社区。定期 NDEx的软件版本将继续扩展其功能。有针对性的服务器硬件升级将 提高容量和性能，以适应NDEx日益增长的使用。 2.扩展癌症通路网络的NDEx语料库。我们将继续保持和扩展NDEX 通过外展、合作和自动化文本和图像的癌症收集（NCC）网络语料库 从文献中捕获癌症网络的分析方法。 3.在下一代癌症基因组分析中使用网络。我们将加强网络的使用 在癌症研究界使用的现有组学分析工具中， 利用NDEx功能和数据的工具。 4.启用交互式网络的发布。我们成功地将出版物链接到NDEx 网络，我们将增加新的功能，为作者和读者，以加强传播的互动 网络及其在出版物中的使用。 5.提供支持和培训，跟踪使用情况，并收集反馈。NDEx项目致力于用户 由癌症研究人员的需求及其用户反馈驱动的参与和发展。 通过这些目标，NDEx项目将从系统建设过渡到维持和启用网络 为国家癌症研究所支持的癌症社区提供生物学服务。

THE NETWORK DATA EXCHANGE – A NETWORK COMMONS FOR BIOLOGISTS PROJECT SUMMARY Knowledge of biological networks has been critical to the analysis of big biomedical datasets, including interpretation of the molecular heterogeneity seen within and across tumors. NDEx, the Network Data Exchange (ndexbio.org), is an online commons where scientists find, share, and publicly distribute biological networks. With a previous grant from the Informatics Technology for Cancer Research program (ITCR U24 CA184427), we created the NDEx open-source database platform along with its public website and query system. Further, we enabled interoperability with the Python and R data science platforms and built NDEx seamlessly into the Cytoscape network analysis and visualization ecosystem. NDEx presently serves a large base of users and network content, with approximately 3285 accounts linked to >180,000 networks, of which approximately 6500 are publicly accessible. NDEx is the approved network repository for articles published in the Springer Nature and Public Library of Science (PLoS) families of journals. We are requesting sustained ITCR funding for the NDEx project to maintain, scale, and enhance the NDEx system, meeting the evolving needs of the biomedical research community via the following five Specific Aims: 1. Maintain and scale NDEx and its services to support a large and growing community of users. Regular software releases of NDEx will continue to extend its capabilities. Targeted server hardware upgrades will increase capacity and performance to match the growing use of NDEx. 2. Extend the NDEx corpus of cancer pathway networks. We will continue to maintain and extend the NDEx Cancer Collection (NCC) corpus of networks via outreach, collaborations, and automated text and image analysis methods to capture cancer networks from literature. 3. Enable the use of networks in next-generation cancer genome analysis. We will enhance the use of networks in existing 'omics analysis tools used by the cancer research community and develop and maintain analysis tools that leverage NDEx functionality and data. 4. Enable publishing of interactive networks. Building on our success in enabling publications to link to NDEx networks, we will add new capabilities for authors and readers to enhance the dissemination of interactive networks and their use in publications. 5. Provide support and training, track usage, and gather feedback. The NDEx Project is committed to user engagement and development driven by the needs of cancer researchers and their user feedback. Through these aims, the NDEx project will transition from system-building to sustaining and enabling network biology for the NCI-supported cancer community.