BridgeDb: standardized access to gene, protein and metabolite identifier mapping services

Abstract

AbstractMany interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. 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. BridgeDb provides such an interface layer, in the form of both a Java and REST API.Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service.BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions.We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants.Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. 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. BridgeDb provides such an interface layer, in the form of both a Java and REST API.Because of the standardized interface layer, BridgeDb is not tied to a specific source of mapping information. You can switch easily between flat files, relational databases and several different web services. Mapping services can be combined to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb isn't just yet another mapping service: it tries to build further on existing work, and integrate multiple partial solutions. The framework is intended for customization and adaptation to any identifier mapping service.BridgeDb makes it easy to add an important capability to existing tools. BridgeDb has already been integrated into several popular bioinformatics applications, such as Cytoscape, WikiPathways, PathVisio, Vanted and Taverna. To encourage tool developers to start using BridgeDb, we've created code examples, online documentation, and a mailinglist to ask questions.We believe that, to meet the challenges that are encountered in bioinformatics today, the software development process should follow a few essential principles: user friendliness, code reuse, modularity and open source. BridgeDb adheres to these principles, and can serve as a useful model for others to follow. BridgeDb can function to increase user-friendliness of graphical applications. It re-uses work from other projects such as BioMart and MIRIAM. BridgeDb consists of several small modules, integrated through a common interface (API). Components of BridgeDb can be left out or replaced, for maximum flexibility. BridgeDb was open source from the very beginning of the project. The philosophy of open source is closely aligned to academic values, of building on top of the work of giants.The BridgeDb library is available at "http://www.bridgedb.org":http://www.bridgedb.org.A paper about BridgeDb was published in BMC Bioinformatics, 2010 Jan 4;11(1):5.BridgeDb blog: "http://www.helixsoft.nl/blog/?tag=bridgedb":http://www.helixsoft.nl/blog/?tag=bridgedb