The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.
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DOI：
10.1186/1471-2105-11-5
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发表时间：
2010-01-04
影响因子：
3
通讯作者：
Evelo CT
中科院分区：
文献类型：
--
作者：
van Iersel MP;Pico AR;Kelder T;Gao J;Ho I;Hanspers K;Conklin BR;Evelo CT
许多互补的解决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。工具可以灵活地支持多个映射服务，或者可以组合映射服务以获得更广泛的覆盖范围。这种方法需要工具和映射服务之间的接口层。在这里，我们提出了BridgeDb，基因，蛋白质和代谢物标识符映射的软件框架。该框架提供了一个标准化的接口层，通过该接口层，生物信息学工具可以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提供了它自己的现成的映射服务，包括webservice和本地数据库形式。然而，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分离，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，可在http://www.bridgedb.org上获得。
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.
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影响因子：
46.9
作者：
Le Novère, N;Finney, A;Wanner, BL
通讯作者：
Wanner, BL
影响因子：
3
作者：
Cote, Richard G;Jones, Philip;Martens, Lennart;Kerrien, Samuel;Reisinger, Florian;Lin, Quan;Leinonen, Rasko;Apweiler, Rolf;Hermjakob, Henning
通讯作者：
Hermjakob, Henning
HMDB：人类代谢组数据库。
影响因子：
14.9
作者：
Wishart, David S;Tzur, Dan;Knox, Craig;Eisner, Roman;Guo, An Chi;Young, Nelson;Cheng, Dean;Jewell, Kevin;Arndt, David;Sawhney, Summit;Fung, Chris;Nikolai, Lisa;Lewis, Mike;Coutouly, Marie-Aude;Forsythe, Ian;Tang, Peter;Shrivastava, Savita;Jeroncic, Kevin;Stothard, Paul;Amegbey, Godwin;Block, David;Hau, David D;Wagner, James;Miniaci, Jessica;Clements, Melisa;Gebremedhin, Mulu;Guo, Natalie;Zhang, Ying;Duggan, Gavin E;Macinnis, Glen D;Weljie, Alim M;Dowlatabadi, Reza;Bamforth, Fiona;Clive, Derrick;Greiner, Russ;Li, Liang;Marrie, Tom;Sykes, Brian D;Vogel, Hans J;Querengesser, Lori
通讯作者：
Querengesser, Lori
影响因子：
3
作者：
van Iersel MP;Kelder T;Pico AR;Hanspers K;Coort S;Conklin BR;Evelo C
通讯作者：
Evelo C
影响因子：
3
作者：
Salomonis, Nathan;Hanspers, Kristina;Pico, Alexander R.
通讯作者：
Pico, Alexander R.