Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.
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DOI：
10.1186/s13742-015-0092-3
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发表时间：
2015
期刊：
影响因子：
9.2
通讯作者：
Wilkinson MD
中科院分区：
文献类型：
--
作者：
Aranguren ME;Wilkinson MD
语义网技术已经在生命科学领域得到了广泛的应用，例如通过OpenLifeData这样的数据提供者和通过SADI这样的Web服务框架。最近报道的OpenLifeData2SADI项目提供了通过SADI服务访问庞大的OpenLifeData数据存储的途径。本文描述了如何使用Galaxy生物信息学分析平台将从OpenLifeData2SADI检索到的数据与其他SADI服务合并，从而使该语义数据更适合于复杂的分析。使用一个工作示例演示了这一点，该示例通过包含SADI工具的Docker映像以及构成演示的数据和工作流实现了可分发和可复制。Galaxy和Docker的结合提供了一种基于SADI语义web服务设计模式的解决方案，可以忠实地再现和共享复杂的数据检索和分析工作流。
Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.