A 3D Data Base for Electron Microscopy and Related Fields ofUltrastructure

电子显微镜及超微结构相关领域的3D数据库

• 批准号: 9505600
• 负责人: Joachim Frank
• 金额: $ 5万
• 依托单位: Health Research Incorporated/New York State Department of Health
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-09-15 至 1997-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9505600&HistoricalAwards=false
• 关键词: 3D; Data; Base; Electron; Microscopy

Several techniques of three-dimensional imaging are about to revolutionize the study of macromolecular assemblies, subcellular structures, and their interactions. 3D electron microscopy and confocal light microscopy are obvious examples. These techniques produce large amounts of data stored in various formats and accessible only through special arrangements with the authors. Only few aspects of a structure represented by a low-resolution density distribution can be captured in scientific publications. There is a large potential for "data mining" by other researchers within the same field or overlapping fields that is currently unused because the data are virtually inaccessible. With this application to the Databases Activities Program of NSF, the PI wishes to continue and expand a joint US-Europe initiative for the establishment of a distributed database that would accommodate ANY low-resolution (non-atomic) 3D data produced by using various experimental methods (EM, LM, x-ray, etc.). The proposal builds on an existing prototype that was developed jointly by the PI and Dr. Jose Maria Carazo in Madrid and that is already publicly accessible through Mosaic/WWW. According to the proposal, Dr. Carazo will visit the Wadsworth Center twice, for a period of five months each, to continue the design and testing of the distributed database and associated software tools, in close interaction with the PI and his group. A graduate student in Computer Science, who will be supervised by the PI and Dr. Daniel Rosenkrantz at SUNY, will design new tools allowing segmentation data to be entered and used in complex 3D data queries, as for instance required in docking of two low-resolution structures, or in the comparison of two structures that have a part-whole relationship. We plan to organize a workshop in mid-term (to be jointly funded by the European Government) that will bring together scientists from centers of 3D ultrastructural imaging and specialists in the areas of scienti fic databases and networking. With the workshop we seek to solicit critical input and start a discussion on how responsibilities might best be shared in the screening of data and how to ensure continuity of the endeavor.

几种三维成像技术将彻底改变大分子组装、亚细胞结构及其相互作用的研究。三维电子显微镜和共聚焦光学显微镜就是明显的例子。这些技术产生以各种格式存储的大量数据，只有通过与作者的特殊安排才能访问这些数据。科学出版物中只能捕捉到低分辨率密度分布所代表的结构的几个方面。在同一领域或重叠领域的其他研究人员进行“数据挖掘”的潜力很大，因为这些数据实际上是不可访问的，目前尚未使用。通过向国家科学基金会的数据库活动计划申请，PI希望继续并扩大美欧联合倡议，建立一个分布式数据库，该数据库将容纳使用各种实验方法（EM， LM， x射线等）产生的任何低分辨率（非原子）3D数据。该提案建立在由PI和马德里的Jose Maria Carazo博士共同开发的现有原型之上，并且已经通过Mosaic/WWW公开访问。根据提案，Carazo博士将两次访问Wadsworth中心，每次为期五个月，继续设计和测试分布式数据库和相关软件工具，与PI及其团队密切互动。在PI和纽约州立大学Daniel Rosenkrantz博士的指导下，一名计算机科学研究生将设计新的工具，允许将分割数据输入并用于复杂的3D数据查询，例如需要对接两个低分辨率结构，或者比较两个具有部分-整体关系的结构。我们计划在中期组织一次研讨会（由欧洲政府共同资助），将来自3D超微结构成像中心的科学家和科学数据库和网络领域的专家聚集在一起。通过讲习班，我们寻求征求关键的投入，并开始讨论如何在筛选数据方面最好地分担责任，以及如何确保这项努力的连续性。