BioXSD: the common data-exchange format for everyday bioinformatics web services
BioXSD: the common data-exchange format for everyday bioinformatics web services
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DOI：
10.1093/bioinformatics/btq391
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发表时间：
2010-09-01
期刊：
影响因子：
5.8
通讯作者：
Jonassen, Inge
中科院分区：
文献类型：
--
作者：
Kalas, Matus;Puntervoll, Pal;Jonassen, Inge
动机：世界各地的生命科学家可以使用大量的公共生物信息学数据库和工具，这些数据库和工具是使用不同的技术和设计开发和部署的。越来越多的资源提供可编程的Web服务接口。然而，有效利用的资源是阻碍了缺乏广泛使用的，标准的数据交换格式的基本，日常的bioinformatics数据types.Results：BioXSD已开发为一个候选人的标准，规范的交换格式的基本生物信息学数据。BioXSD由专用的XML Schema表示，并定义了生物序列、序列注释、比对和资源引用的语法。我们已经采用了一组Web服务，使用BioXSD作为输入和输出格式，并实现了一个测试用例的工作流程。这表明该方法是可行的，并提供流畅的互操作性。BioXSD的语义由埃达姆本体的注释提供。我们将在单独的一节中讨论BioXSD与其他计划和方法的关系，包括现有的标准和语义Web。
Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types.Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web.