Posts Tagged ‘publication’

BridgeDb paper published

Tuesday, January 12th, 2010

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.

Mining biological pathways using WikiPathways web services

Thursday, August 6th, 2009

A website lets people interact with computers over the Internet. A web service on the other hand, lets computers interact with computers over the Internet. We’ve created a web service for WikiPathways so people can write computer scripts to do interesting new things with WikiPathways. This is all described in great detail in an article that was recently published in PLoS One.

Mining biological pathways using WikiPathways web services.
Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR.
PLoS One. 2009 Jul 30;4(7):e6447.

Naturally it’s open access, so you can read it all online. From the article:

The WikiPathways web service provides an interface for programmatic access to community-curated pathway information. […] The web service can be used by software developers to build or extend tools for analysis and integration of pathways, interaction networks and experimental data. The web services are also useful for assisting and monitoring the community-based curation process. By providing this web service, we hope to help researchers and developers build tools for pathway-based research and data analysis.

Automated access, plus the fact that all content is available under a Creative Commons license, should make WikiPathways even more useful as a scientific resource. It will be interesting to see what kind of uses people will come up with.