A web services choreography scenario for interoperating bioinformatics applications.
A web services choreography scenario for interoperating bioinformatics applications.
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DOI：
10.1186/1471-2105-5-25
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发表时间：
2004-03-10
影响因子：
3
通讯作者：
Cheung KH
中科院分区：
文献类型：
--
作者：
de Knikker R;Guo Y;Li JL;Kwan AK;Yip KY;Cheung DW;Cheung KH
全基因组数据分析往往需要多个数据库和分析工具的互操作。大量的基因组数据库和生物信息学应用程序可以通过网络获得，但很难实现互操作的自动化，因为：1)运行应用程序的平台是异质的，2)它们的网络接口对机器不友好，3)它们使用非标准格式的数据输入和输出，4)它们没有利用标准来定义应用程序接口和消息交换，以及5)现有的用于远程消息传递的协议通常不是防火墙友好的。为了克服这些问题，Web服务已经成为用于异类应用程序之间消息交换的基于XML的标准模型。已经开发了Web服务引擎来管理Web服务工作流的配置和执行。为了证明使用Web服务比使用传统Web界面的好处，我们比较了HAPI的两种实现，HAPI是加州大学圣地亚哥分校(UCSD)开发的一种基因表达分析实用程序，它允许基于生物医学文献对基因组或基因簇进行可视化表征。该实用程序将一组微阵列斑点ID作为输入，并输出与输入相关的MESH关键字层次结构，并按医学主题标题(MESH)类别进行分组。虽然人类很容易将HTML输出可视化，但计算机应用程序很难从语义上进行解释。为了促进机器处理能力，我们创建了一个由三个复制HAPI功能的Web服务组成的工作流。这些Web服务使用文档式消息，这意味着消息以基于XML的格式编码。我们比较了实现基于XML的工作流的三种方法：硬编码的Java应用程序、Collaxa BPEL服务器和Taverna工作台。Java程序充当Web服务引擎，并使用Web服务编排语言(BPEL4WS)与这些Web服务进行互操作。虽然实现和发布Web服务相对简单，但Web服务编排引擎的使用仍处于初级阶段。然而，整个行业对Web服务标准的支持和推动正在迅速增加使用Web服务来统一异类生物信息学应用程序的成功机会。由于当前可用的Web服务引擎还不成熟，通过将工作流硬编码为Java应用程序来实现简单的、特别的、基于XML的工作流仍然是最实用的。对于高级Web服务用户，Collaxa BPEL引擎促进了配置和管理环境，该环境可以完全处理基于XML的工作流。
Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow.
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