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首页> 外文期刊>Journal of Clinical Bioinformatics >An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature
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An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature

机译：eUtils工具集及其用于创建将基因组学和蛋白质组学分析与特定领域的生物医学文献联系起来的管道的用途

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Background Numerous biomedical software applications access databases maintained by the US National Center for Biotechnology Information (NCBI). To ease software automation, NCBI provides a powerful but complex Web-service-based programming interface, eUtils. This paper describes a toolset that simplifies eUtils use through a graphical front-end that can be used by non-programmers to construct data-extraction pipelines. The front-end relies on a code library that provides high-level wrappers around eUtils functions, and which is distributed as open-source, allowing customization and enhancement by individuals with programming skills. Methods We initially created an application that queried eUtils to retrieve nephrology-specific biomedical literature citations for a user-definable set of genes. We later augmented the application code to create a general-purpose library that accesses eUtils capability as individual functions that could be combined into user-defined pipelines. Results The toolset’s use is illustrated with an application that serves as a front-end to the library and can be used by non-programmers to construct user-defined pipelines. The operation of the library is illustrated for the literature-surveillance application, which serves as a case-study. An overview of the library is also provided. Conclusions The library simplifies use of the eUtils service by operating at a higher level, and also transparently addresses robustness issues that would need to be individually implemented otherwise, such as error recovery and prevention of overloading of the eUtils service.
机译：背景技术许多生物医学软件应用程序访问由美国国家生物技术信息中心（NCBI）维护的数据库。为了简化软件自动化，NCBI提供了功能强大但复杂的基于Web服务的编程接口eUtils。本文介绍了一个工具集，该工具集通过图形前端简化了eUtils的使用，非程序员可以使用该前端来构建数据提取管道。前端依赖于一个代码库，该代码库提供围绕eUtils函数的高级包装，并作为开源分发，从而允许具有编程技能的个人进行自定义和增强。方法我们最初创建了一个查询eUtils的应用程序，以检索用户定义的一组基因的肾病学特定生物医学文献引文。后来，我们扩展了应用程序代码，以创建一个通用库，该库以单独的功能访问eUtils功能，这些功能可以组合到用户定义的管道中。结果该工具集的用法通过一个应用程序进行了说明，该应用程序充当该库的前端，非程序员可以使用它来构建用户定义的管道。该库的操作针对文献监视应用程序进行了说明，该应用程序是一个案例研究。还提供了该库的概述。结论该库通过更高级别的操作简化了eUtils服务的使用，并且透明地解决了健壮性问题，这些问题否则需要单独实现，例如错误恢复和防止eUtils服务超载。

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