Abstract：
Enzymes catalyze diverse biochemical reactions and are building blocks of cellular and metabolic pathways. Data and metadata of enzymes are distributed across databases and are archived in various formats. The enzyme databases provide utilities for efficient searches and downloading enzyme records in batch mode but do not support organism-specific extraction of subsets of data. Users are required to write scripts for parsing entries for customized data extraction prior to downstream analysis. Integrated Customized Extraction of Enzyme Data (iCEED) has been developed to provide organism-specific customized data extraction utilities for seven commonly used enzyme databases and brings these resources under an integrated portal. iCEED provides dropdown menus and search boxes using typehead utility for submission of queries as well as enzyme class-based browsing utility. A utility to facilitate mapping and visualization of functionally important features on the three-dimensional (3D) structures of enzymes is integrated. The customized data extraction utilities provided in iCEED are expected to be useful for biochemists, biotechnologists, computational biologists, and life science researchers to build curated datasets of their choice through an easy to navigate web-based interface. The integrated feature visualization system is useful for a fine-grained understanding of the enzyme structure-function relationship. Desired subsets of data, extracted and curated using iCEED can be subsequently used for downstream processing, analyses, and knowledge discovery. iCEED can also be used for training and teaching purposes.
摘要：
酶催化多种生化反应，是细胞和代谢途径的组成部分。酶的数据和元数据分布在数据库中，并以各种格式存档。酶数据库提供了用于以批量模式进行高效搜索和下载酶记录的实用程序，但不支持特定于生物体的数据子集提取。在下游分析之前，用户需要编写脚本来解析条目以进行自定义数据提取。已开发出集成定制酶数据提取（iCEED），为七个常用的酶数据库提供特定于生物体的定制数据提取实用程序，并将这些资源置于集成门户下。iCEED使用typehead实用程序提供下拉菜单和搜索框，用于提交查询以及基于酶类的浏览实用程序。集成了促进酶的三维（3D）结构上功能重要特征的映射和可视化的实用程序。iCEED中提供的定制数据提取实用程序有望对生物化学家有用，生物技术专家,计算生物学家，和生命科学研究人员通过易于导航的基于Web的界面来构建他们选择的精选数据集。集成的特征可视化系统对于对酶结构-功能关系的细粒度理解很有用。所需的数据子集，使用iCEED提取和策划可随后用于下游处理，分析，和知识发现。iCEED也可用于培训和教学目的。
