The Network Data Exchange - a Network Commons for Biologists

网络数据交换 - 生物学家的网络共享空间

• 批准号: 10645935
• 负责人: Dexter Pratt
• 金额: $ 84.9万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-04-15 至 2028-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10645935
• 关键词: Atlas of Cancer Mortality in the United States; Biological; Biology; Biomedical Research; Cancer Biology; Cancer Research Project; Collaborations; Collection; Communities; Computer software; Data; Data Analyses; Data Science; Data Set; Databases; Destinations; Development; Disease; Documentation; Ecosystem; Evolution; Family; Feedback; Funding; Grant; Heterogeneity; Image Analysis; Informatics; Internet; Java; Journals; Knowledge; Library Science; Licensing; Link; Literature; Malignant Neoplasms; Maps; Methods; Molecular; Nature; Pathway Analysis; Pathway interactions; Performance; Play; Publications; Published Comment; Publishing; Pythons; Reader; Research Personnel; Role; Scientist; Series; Services; System; Technology; Time; Training; Update; Visualization; Visualization software; anticancer research; automated text message; base; big biomedical data; cancer genome; data exchange; data exchange system; genome analysis; interoperability; meetings; next generation; novel; open source; outreach; recruit; repository; success; tool; tool development; tumor; web site

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.

网络数据交换——生物学家的网络共享 项目概要 生物网络知识对于分析大型生物医学数据集至关重要，包括 解释肿瘤内部和肿瘤之间的分子异质性 NDEx（网络数据交换）。 (ndexbio.org) 是一个在线共享资源，科学家可以在这里查找、共享和公开分发生物网络。 借助癌症研究信息技术计划 (ITCR U24 CA184427) 的先前资助， 我们创建了 NDEx 开源数据库平台及其公共网站和查询系统。 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目前为大量用户提供服务。 网络内容，大约 3285 个帐户链接到超过 180,000 个网络，其中大约 6500 个 NDEx 是 Springer Nature 上发表的文章的批准网络存储库。 和公共科学图书馆 (PLoS) 期刊系列。 我们请求为 NDEx 项目提供持续的 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常规用户社区。 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。 提高容量和性能以适应 NDEx 不断增长的使用。 2. 扩展癌症通路网络的 NDEx 语料库 我们将继续维护和扩展 NDEx。 通过外展、协作以及自动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. 促进网络在下一代癌症基因组分析中的应用 我们将加强网络的使用。 癌症研究界使用的现有“组学分析工具”，并开发和维护分析 利用 NDEx 功能和数据的工具。 4. 在我们成功将出版物链接至 NDEx 的基础上，实现交互式网络的发布。 网络方面，我们将为作者和读者添加新的能力，增强传播互动 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 NCI 支持的癌症界的生物学。