The Donnelly Centre, University of Toronto, ON, Canada.
Database (Oxford). 2011 Jan 12;2011:baq037. doi: 10.1093/database/baq037. Print 2011.
The Biomolecular Interaction Network Database (BIND) is a major source of curated biomolecular interactions, which has been unmaintained for the last few years, a trend which will eventually result in the loss of a significant amount of unique biomolecular interaction information, mostly as database identifiers become out of date. To help reverse this trend, we converted BIND to a standard format, Proteomics Standard Initiative-Molecular Interaction 2.5, starting from the last curated data release (from 2005) available in a custom XML format and made the core components (interactions and complexes) plus additional valuable curated information available for download (http://download.baderlab.org/BINDTranslation/). Major work during the conversion process was required to update out of date molecule identifiers resulting in a more comprehensive conversion of BIND, by measures including number of species and interactor types covered, than what is currently accessible elsewhere. This work also highlights issues of data modeling, controlled vocabulary adoption and data cleaning that can serve as a general case study on the future compatibility of interaction databases. Database URL: http://download.baderlab.org/BINDTranslation/
生物分子相互作用网络数据库（BIND）是经过精心整理的生物分子相互作用的主要来源，它已经有好几年没有得到维护了，这种趋势最终将导致大量独特的生物分子相互作用信息丢失，主要是因为数据库标识符已经过时。为了帮助扭转这一趋势，我们将 BIND 转换为标准格式，即蛋白质组学标准倡议-分子相互作用 2.5，从可用的自定义 XML 格式的最后一个经过精心整理的数据版本（来自 2005 年）开始，并提供核心组件（相互作用和复合物）以及其他有价值的经过整理的信息供下载（http://download.baderlab.org/BINDTranslation/）。在转换过程中需要进行大量工作来更新过时的分子标识符，从而使 BIND 的转换更加全面，从涵盖的物种和相互作用物类型的数量等方面来看，都比其他地方目前可以访问的信息更加全面。这项工作还突出了数据建模、控制词汇采用和数据清理等问题，这些问题可以作为交互数据库未来兼容性的一般案例研究。数据库网址：http://download.baderlab.org/BINDTranslation/
