COMMUNITY DEVELOPMENT OF THE CELL-CENTERED DATABASE

以细胞为中心的数据库的社区开发

• 批准号: 8856581
• 负责人: Mark H Ellisman
• 金额: $ 30.37万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-30 至 2016-09-05
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8856581
• 关键词: Ally; American; Architecture; Atlases; Award; Big Data; Binding; Biomedical Research; Cell model; Cell physiology; Cells; Cellular Structures; Cellular biology; Code; Collaborations; Communities; Community Developments; Computer software; Data; Data Set; Databases; Development; Documentation; Education; Electron Microscopy; Electrons; Environment; Explosion; Funding; Future; Growth; Health; Hybrid Cells; Image; Imagery; Imaging Device; Individual; Internet; Investigation; Joints; Libraries; Light; Link; Maintenance; Metadata; Microscopic; Microscopy; Modality; Modeling; Molecular; Molecular Structure; Morphology; National Institute of General Medical Sciences; Neurosciences; Online Systems; Ontology; Organism; Phenotype; Research Infrastructure; Research Personnel; Resources; Semantics; Services; Societies; Software Tools; Solutions; Speed; Structure; System; Three-Dimensional Imaging; Tissues; Voting; Work; animation; base; cell type; cellular imaging; cost; data management; data sharing; design; design and construction; federated computing; flexibility; improved; information framework; insight; instrumentation; knowledge base; light microscopy; open source; programs; reconstruction; repository; social networking website; software development; system architecture; tool

DESCRIPTION (provided by applicant): This proposal outlines plans for continued development and maintenance of the OpenCCDB software suite, a set of tools for web-based management, visualization and annotation of large multidimensional light and electron microscopic imaging data sets. Modern analytical and molecularly-based biomedical investigations increasingly draw upon multiscale and multimodal cell-centered imaging to gain insight into spatially constrained interactions of molecular machinery of cells and tissues. The OpenCCDB was developed under the auspices of the Cell Centered Database (CCDB0 project, an on-line repository and platform for sharing microscopic imaging data of cells and tissues. The CCDB project was predicated on developing solutions for federating access to very large 3D imaging data sets, produced by diverse instrumentations and maintained across diverse technological platforms. The CCDB model is built on flexible and expandable data stores that can be fielded globally but accessed through CCDB's central metadata system and linked through data federations like the Neuroscience Information Framework (http://neuinfo.org). During the last funding period, the American Society for Cell Biology launched its own data repository, with support from ARRA funding. The Cell: An Image Library currently contains > 37,000 exemplary imaging data sets from light and electron microscopy, all available through an elegant cell-centered user interface. To provide a more unified and sustainable resource for research and education, the ASCB Council and Executive Committee voted in 2011 to partner their effort with the group at UCSD, combining their curatorial and interface design expertise and accomplishments with UCSD's database and software development expertise and accomplishments. In so doing, ASCB transitioned control of the development and future sustainability of their user portal environment, "The Cell:An Image Library" to the CCDB team at UCSD. Immediately, this new alliance applied CCDB's open source software framework, OpenCCDB, to the task of extending the functionality of The Cell: An Image Library system, adding new capability to upload and explore massive datasets, facilitate data sharing, and completely federate its underlying database with the CCDB. The resultant integrated environment offers the scientific community a more comprehensive solution to propel cell-centric biomedical research and education than that offered previously. In this proposal, we outline aims to develop and deploy additional personalized data management and annotation tools within the context of The Cell: An Image Library, by combining the power and tools of a social networking site with specialized tools for web-based management, sharing, annotation and federation of very large microscopic imaging data sets.

描述（由申请人提供）：该提案概述了OpenCCDB软件套件的持续开发和维护的计划，这是一组用于基于Web的管理的工具，可视化和注释大型多维光和电子显微镜成像数据集。现代的分析和基于分子的生物医学研究越来越多地利用多尺度和多模式的以细胞为中心的成像，以深入了解细胞和组织分子机械的空间约束相互作用。 OpenCCDB是在中心数据库的主持下开发的（CCDB0项目，一个在线存储库和平台，用于共享细胞和组织的显微镜成像数据。CCDB项目是基于开发解决方案，以开发解决方案，用于开发联合会访问非常大的3D成像数据集，由多样化的仪表置于多样性的范围内，并跨越了多样化的仪表型，并跨越了多样化的技术。可以通过CCDB的中央元数据系统访问的商店，并通过Neuroscience信息框架（http://neuinfo.org）链接，在上次融资期间显微镜，所有这些都可以通过优雅的以细胞为中心的用户界面获得，以提供更统一的可持续资源来进行研究和教育，ASCB委员会和执行委员会在2011年投票通过与UCSD的小组合作，将其策展和界面设计专业知识与成就结合在一起。这样一来，ASCB将其用户门户网站环境的发展和未来可持续性的控制权转移给了UCSD的CCDB团队。该新联盟立即应用了CCDB的开源软件框架OpenCCDB，以扩展单元格的功能：图像库系统，为上传和探索大量数据集添加了新功能，便利数据共享，并与CCDB完全联合其基础数据库。由此产生的综合环境为科学界提供了一种比以前提供的更全面的解决方案，用于推动以细胞为中心的生物医学研究和教育。在此建议中，我们概述旨在通过将社交网站的功率和工具与用于基于Web的管理，共享，注释，注释和联合非常大的显微镜成像数据集的专门工具，在单元格库的背景下开发和部署其他个性化数据管理和注释工具。