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 项目摘要 对生物网络的了解对于分析大型生物医学数据集至关重要，包括 跨肿瘤内外看到的分子异质性的解释。 NDEX，网络数据交换 （ndexbio.org）是一个在线公共场所，科学家在其中找到，共享和公开分发生物网络。 凭借Informatics for Cancer研究计划（ITCR U24 CA184427）的赠款， 我们与公共网站和查询系统一起创建了NDEX开源数据库平台。此外， 我们启用了与Python和R数据科学平台的互操作性，并无缝地构建了NDEX 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，大约有3285个帐户链接到> 180,000个网络，其中约为6500个帐户 可以公开访问。 NDEX是Springer Nature发表的文章的批准网络存储库 以及期刊的公共科学图书馆（PLOS）家族。 我们要求为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来满足生物医学研究界不断发展的需求： 1。维护和扩展NDEX及其服务，以支持大型且不断增长的用户社区。常规的 NDEX的软件发行将继续扩展其功能。目标服务器硬件升级将 提高容量和性能以符合NDEX日益增长的使用。 2。扩展癌症途径网络的NDEX语料库。我们将继续维护和扩展NDEX 通过外展，合作以及自动化文本和图像的网络癌症收集（NCC）语料库 分析方法是从文献中捕获癌症网络的方法。 3。在下一代癌症基因组分析中使用网络。我们将增强网络的使用 在现有的“ OMICS分析工具”中，癌症研究界使用并开发和维护分析 利用NDEX功能和数据的工具。 4。启用交互式网络的发布。基于我们成功使出版物链接到NDEX的成功建立 网络，我们将为作者和读者添加新的功能，以增强交互式的传播 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 癌症研究人员及其用户反馈的需求驱动的参与和发展。 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支持的癌症社区的生物学。