Organelle DB / Organelle View: A Community Resource of Protein Localization and Function

密歇根大学安阿伯分校获得了一笔赠款，以进一步开发细胞器DB，一个网络访问的关系数据库，汇编了细胞器定位蛋白质和主要蛋白质复合物的补充清单。细胞器数据库包含来自真核生物王国的154种生物的25，000种蛋白质的数据。细胞器DB中的每种蛋白质都提供了其亚细胞定位，蛋白质序列以及其功能的详细描述（如可用）（从相应的模式生物数据库中挑选）。为了促进数据的互操作性，所有蛋白质定位都使用来自基因本体论联盟的受控词汇表进行注释。细胞器数据库也是一个重要的生物图像库，提供了大约1500张携带染色蛋白质的酵母细胞的显微照片。细胞器数据库可在organelledb.lsi.umich.edu免费访问。目前，细胞器数据库是一个跨物种和跨学科的资源，巩固了我们的知识，包括真核细胞器和亚细胞结构的蛋白质;然而，它持有的潜力要多得多。细胞器数据库可以作为一个渠道，通过它，我们可以提供一个集成的知识库的orthopathic数据集相关的蛋白质定位，同时促进使用标准化的数据格式和图形界面的开发，以可视化的生物数据在非文本为基础的格式。在这个奖项中，Organelle DB将与相关的外部数据库集成。来自蛋白质-蛋白质相互作用研究的Orthopathy数据集将通过与BIND数据库的链接与细胞器DB中的蛋白质定位数据相结合。通过活细胞荧光显微镜可视化的真核蛋白质的图像将使用开放显微镜环境（OME）的标准化数据结构并入细胞器DB中。细胞器视图是一个以非文本格式显示本地化数据的原型界面，将通过细胞器数据库访问。细胞器视图被设想为一个特别有用的资源，在教学中的年轻学生（例如，高中生物学生和大学本科生），通过一个视觉上引人注目和“有趣”的界面向他们介绍细胞和分子生物学中的复杂概念。

The University of Michigan at Ann Arbor is awarded a grant to further develop Organelle DB, a Web-accessible relational database compiling a supplemented listing of organelle-localized proteins and major protein complexes. Organelle DB houses data for 25,000 proteins from 154 organisms spanning the eukaryotic kingdom. Each protein in Organelle DB is presented with its subcellular localization, protein sequence and, as available, a detailed description of its function (as culled from corresponding model organism databases). To facilitate data interoperability, all protein localizations are annotated using controlled vocabulary from the Gene Ontology consortium. Organelle DB is also a significant repository of biological images, providing roughly 1500 micrographs of yeast cells carrying stained proteins. Organelle DB is freely accessible at organelledb.lsi.umich.edu. At present, Organelle DB is a cross-species and cross-discipline resource consolidating our knowledge of the proteins comprising eukaryotic organelles and subcellular structures; however, it holds the potential to be much more. Organelle DB can serve as a channel through which we can provide an integrated knowledge base of orthologous data sets related to protein localization, while fostering the use of standardized data formats and the development of graphical interfaces for the visualization of biological data in non-text-based formats. In this award Organelle DB will be integrated with relevant external databases. Orthologous data sets from protein-protein interaction studies will be integrated with protein localization data in Organelle DB through links to and from the BIND database. Images of eukaryotic proteins visualized by live cell fluorescence microscopy will be incorporated into Organelle DB using the standardized data structure of the Open Microscopy Environment (OME). Organelle View, a prototype interface for the visualization of localization data in a non text-based format, will be made accessible through Organelle DB. Organelle View is envisioned as a particularly useful resource in the instruction of younger students (e.g., high school biology students and college undergraduates), introducing them to complicated concepts in cellular and molecular biology through an interface that is visually arresting and "fun".