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Bioinformatics nation

At TDWG 2009 , which ended about two hours ago, I learned of Lincoln Stein’s 2002 paper Creating a bioinformatics nation. It’s not open access so I haven’t read it yet, but one can get the gist here and here. The talk/paper was apparently influential (to those better clued in than me), and I’ve added it to the Neurocommons reading list. The main message is: Don’t make us screen-scrape; provide machine-friendly access to your stuff.

I’m not too keen on web services with fancy APIs; REST-based query interfaces, bulk downloads, and SPARQL seem to be easier to use. But the idea is right.

Has there been any progress since 2002?

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Categories: Uncategorized
  1. 2009-11-22 at 22:25

    My friend Shaun in my old lab has set up a Galaxy server recently, and is completely loving it. There are several more tools out there that perform similar functions. I think that providing open data download points (REST, SPARQL, whatever) only solves about 10% of the problem, but it’s a good start…

  2. 2009-11-24 at 01:03

    Cool, hadn’t known about that one. http://www.myexperiment.org/ and http://www.biomoby.org/ are along the same lines. It’s not coincidental that both projects are fond of the LSID story, which features analysis repeatability enabled by object immutability, although Galaxy is the first I’ve heard of anyone really making good use of such a feature.

    I can’t help feeling that access to data is always the necessary starting point, and no tool will make up for want of the information you need as input. That’s why I focus on access to information, rather than tools. Tools don’t require coordination; access does.

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