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

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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".