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

密歇根大学安娜堡分校获得一笔赠款，用于进一步开发Organelle DB，这是一个可通过Web访问的关系数据库，汇编了细胞器局部蛋白质和主要蛋白质复合体的补充列表。细胞器DB保存了来自真核王国154种生物的25,000种蛋白质的数据。Organelle DB中的每个蛋白质都有它的亚细胞定位、蛋白质序列和详细的功能描述(从相应的模式生物数据库中挑选出来)。为了促进数据的互操作性，所有的蛋白质定位都使用来自基因本体论联盟的受控词汇进行注释。细胞器DB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上免费访问。目前，Organelle DB是一个跨物种和跨学科的资源，巩固了我们对组成真核细胞器和亚细胞结构的蛋白质的知识；但它拥有更多的潜力。细胞器数据库可以作为一个渠道，通过它我们可以提供与蛋白质定位相关的直系数据集的完整知识库，同时促进标准化数据格式的使用和非基于文本格式的生物数据可视化图形界面的开发。在这个奖项中，Organelle DB将与相关的外部数据库整合。来自蛋白质-蛋白质相互作用研究的同源数据集将通过与BIND数据库的链接与Organelle DB中的蛋白质定位数据相结合。通过活细胞荧光显微镜显示的真核蛋白质图像将使用开放显微镜环境(OME)的标准化数据结构合并到Organelle DB中。Organelle View是以非文本格式可视化本地化数据的原型界面，将通过Organelle DB访问。细胞器视图被认为是指导年轻学生(例如，高中生和大学本科生)的一个特别有用的资源，通过一个视觉上吸引人的“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".