The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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.
van Iersel
Martijn P
MP
Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, the Netherlands. martijn.vaniersel@bigcat.unimaas.nl
Pico
Alexander R
AR
Kelder
Thomas
T
Gao
Jianjiong
J
Ho
Isaac
I
Hanspers
Kristina
K
Conklin
Bruce R
BR
Evelo
Chris T
CT
D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods; D016247:Information Storage and Retrieval; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
D011506:Proteins