Department of Computer Science, University of South Dakota, 414 East Clark St., Vermillion, SD 57069, USA.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):12-24. doi: 10.1109/TCBB.2008.98.
Many in silico investigations in bioinformatics require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community databases, and project databases for use in domain-specific research. Different data sources frequently utilize distinct query languages and return results in unique formats, and therefore researchers must either rely upon a small number of primary data sources or become familiar with multiple query languages and formats. Similarly, the associated analytic tools often require specific input formats and produce unique outputs which make it difficult to utilize the output from one tool as input to another. The BioExtract Server (http://bioextract.org) is a Web-based data integration application designed to consolidate, analyze, and serve data from heterogeneous biomolecular databases in the form of a mash-up. The basic operations of the BioExtract Server allow researchers, via their Web browsers, to specify data sources, flexibly query data sources, apply analytic tools, download result sets, and store query results for later reuse. As a researcher works with the system, their "steps" are saved in the background. At any time, these steps can be preserved long-term as a workflow simply by providing a workflow name and description.
许多生物信息学中的计算机模拟研究都需要访问多个分布式数据源和分析工具。必要的数据源可能包括大型公共数据存储库、社区数据库以及用于特定领域研究的项目数据库。不同的数据源通常使用不同的查询语言，并以独特的格式返回结果，因此研究人员必须要么依赖少数主要数据源，要么熟悉多种查询语言和格式。同样，相关的分析工具通常需要特定的输入格式，并产生独特的输出，这使得很难将一个工具的输出用作另一个工具的输入。BioExtract Server（http://bioextract.org）是一个基于 Web 的数据集成应用程序，旨在以混搭的形式整合、分析和提供来自异构生物分子数据库的数据。BioExtract Server 的基本操作允许研究人员通过其 Web 浏览器指定数据源、灵活查询数据源、应用分析工具、下载结果集，并存储查询结果以备将来重用。当研究人员使用该系统时，他们的“步骤”会在后台保存。在任何时候，只要提供工作流名称和描述，这些步骤就可以作为工作流长期保存。
