Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, the Netherlands.
BMC Bioinformatics. 2010 Jan 4;11:5. doi: 10.1186/1471-2105-11-5.
Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services.
Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications.
By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.
有许多补充方案可用于标识符映射问题。这为生物信息学工具开发人员创造了机会。可以制作工具以灵活支持多个映射服务，或者可以组合映射服务以获得更广泛的覆盖范围。这种方法需要在工具和映射服务之间使用接口层。
在这里，我们展示了 BridgeDb，这是一个用于基因、蛋白质和代谢物标识符映射的软件框架。该框架通过提供标准化的接口层，使生物信息学工具能够连接到不同的标识符映射服务。这种方法使工具开发人员更容易支持标识符映射。映射服务可以组合或合并，以支持多组学实验或集成自定义微阵列注释。BridgeDb 提供了自己的即用型映射服务，既有 Web 服务形式，也有本地数据库形式。但是，该框架旨在定制和适应任何标识符映射服务。BridgeDb 已经集成到几个生物信息学应用程序中。
通过将生物信息学工具与映射服务解耦，BridgeDb 提高了这些工具的功能和灵活性。所有描述的软件都是开源的，并可在 http://www.bridgedb.org 上获得。
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