Bringing Open Source To Biomedicine

waderoush writes "'Facebook and Twitter may have proven that humans have a deep-seated desire for sharing, [but] this impulse is still widely suppressed in biomedicine,' biotech reporter Luke Timmerman observes in this column on Sage Bionetworks founder Stephen Friend. Friend is working to convince drugmakers and academic researchers to pool their experimental genomic data in a shared database called the Sage Commons. The database could be used to track adverse drug events, or to 'visually display network models of disease that connect the dots between genes, proteins, and clinical manifestations of disease in ways that [scientific] journals are not equipped to handle,' Timmerman says. Researchers from Stanford, Columbia, UCSF, and UCSD are already contributing to the Sage Commons, and Friend is now calling for a community effort by drugmakers, academic scientists, doctors, regulators, insurers, and patients to 'grab this platform and run with it on their own."

Comments

Re:So long as there is money to be made

[sexconker]

I can tell you didn't RTFA, or even RTFS.
TFH is fucking misleading.

There is very little to do with open source, or openness in general.

Some guy is simply trying to get various players to buy into his system, with money and data, so he can then go back and run a few queries, maybe make a little graph, etc., and sell that data to others (for the price of money and more data).

It's basically stone soup, but he demands money as well as all the work. (And if he's not demanding money now, just wait until the date draws nearer.)

But this will never happen. The reason these companies are so tight lipped with their data is not because they don't see a benefit in sharing and accessing data, but because they don't dare let others see their dirty laundry, lest they expose themselves as liable for their fuckups.

Re:Incorporating this "Standard"

[Samantha Wright]

Well, although you're right, there is still something that I believe is usually called a "clusterfuck" when it comes to data transfer formats for biology and chemistry, and it's not helping the open-ification process any. (Note that this list seems to omit most of the proprietary formats, at least a dozen of which I can name off the top of my head.) It's symptomatic of the commercial land-grab that took place in biomedical computing (mostly) in the nineties.