I’m very happy that our paper on BridgeDb was accepted by BMC Bioinformatics. It’s open access so download it to your hearts content. BridgeDb is all about identifier mapping, which I blogged about before (here, here and here).
BridgeDb lets you find cross-references for identifiers, but BridgeDb is not simply a cross-reference database. BridgeDb provides a standard method to access other cross-reference databases. And because of that level of standardization, you can easily decide to switch to a different source of cross-references.
Deepak Singh uses the term “middleware”, which is a good way to explain it, if that sort of word means anything to you.
But let me try to explain in a different way. BirdgeDb is really a travel adapter. Suppose you’re in Japan and you’ve brought some gear like a laptop, cell phone and a nintendo DS (just in case you get stuck in a blizzard while transferring at CDG). Much to your dismay you discover, after checking into your hotel, that none of your plugs fit in Japanese electrical sockets. So what do you do? Do you go down to Akihabara and spend a grand on a new laptop, phone and portable video game unit? Or do you buy a travel adapter for $1.95?
Just like there are many different power plugs around the world, there are many databases that do identifier mapping. And just like travel adapters let you plug in your laptop anywhere, no matter what country, BridgeDb lets you use your favorite bioinformatics tool, no matter what the source of identifier mappings is (Provided that the tool uses BridgeDb).
Power plugs around the world
It’s important to realize that BridgeDb is simply a conduit of information. It does not calculate cross-references from scratch, nor does it give any guarantees about the validity of those cross-references. You shouldn’t ask if BridgeDb provides better identifier mappings. That is like asking if a travel adapter provides better electricity. You still depend on the power company to give you a stable source of electricity. The travel plug just gives you flexibility to adapt to different circumstances.
Tags: bridgedb, identifier mapping problem, japan, middleware, publication