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: 8664877
• 负责人: Mark H Ellisman
• 金额: $ 30.49万
• 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 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8664877
• 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; 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; public health relevance; 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. PUBLIC HEALTH RELEVANCE: This renewal application outlines plans to harden and further develop the code base of the Open CCDB software platform in support of the new joint cell-centered microscopy resource established through the merging of the Cell Image Library and the Cell Centered Database.

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计划，OpenCCDB软件套件是一套用于大型多维光和电子显微镜成像数据集的基于网络的管理、可视化和注释的工具。现代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态细胞为中心的成像，以深入了解细胞和组织的分子机制的空间约束相互作用。OpenCCDB是在Cell Centered Database（CCDB0项目）的支持下开发的，CCDB0项目是一个在线存储库和平台，用于共享细胞和组织的显微成像数据。CCDB项目的基础是开发解决方案，用于联合访问由不同仪器产生并在不同技术平台上维护的非常大的3D成像数据集。CCDB模型建立在灵活和可扩展的数据存储基础上，这些数据存储可以在全球部署，但可以通过CCDB的中央元数据系统访问，并通过神经科学信息框架（http：//www.example.com）等数据联合会进行链接。neuinfo.org在上一个资助期间，美国细胞生物学学会在ARRA资金的支持下推出了自己的数据库。细胞：Image Library目前包含超过37，000个来自光学和电子显微镜的示例性成像数据集，所有这些数据都可以通过优雅的以细胞为中心的用户界面获得。为了提供一个更统一和可持续的研究和教育资源，ASCB理事会和执行委员会在2011年投票决定与UCSD的小组合作，将他们的策展和界面设计专业知识和成就与UCSD的数据库和软件开发专业知识和成就相结合。通过这样做，ASCB将其用户门户环境“The Cell：An Image Library”的开发和未来可持续性的控制权移交给了UCSD的CCDB团队。这个新的联盟立即将CCDB的开源软件框架OpenCCDB应用于扩展The Cell：An Image Library系统的功能，增加了上传和探索大量数据集的新功能，促进了数据共享，并将其底层数据库与CCDB完全联合。由此产生的集成环境为科学界提供了一个比以前更全面的解决方案，以推动以细胞为中心的生物医学研究和教育。在这项提案中，我们概述了旨在开发和部署额外的个性化数据管理和注释工具的细胞：一个图像库的背景下，通过结合的权力和工具的社交网站与专门的工具，基于网络的管理，共享，注释和联邦非常大的显微成像数据集。 公共卫生关系：该更新申请概述了加强和进一步开发Open CCDB软件平台代码库的计划，以支持通过合并细胞图像库和细胞中心数据库建立的新联合细胞中心显微镜资源。