Accelerating access to biomedical evidence

The PLoS synergy between open source and biomedical open access

Listen with webreader

I was staring that the bottom of the page for PLoSNTDs (PLoS Neglected Tropical Diseases, the first open-access journal devoted to the world’s most neglected tropical diseases ) after hearing the Editor in Chief Dr. Peter Hotez at MLA2011, the annual meeting of the Medical Library Association.  The lineup of sponsors–

are for the most part recognizable, but I really had no idea what mulgara represented.

mulgaraMulgara is a scalable open source RDF database written entirely in Java.  From the FAQ, I learned that:

  • Mulgara is an Australian marsupial, and is listed as “vulnerable”.  The open source predecessor to Mulgara was Kowari, an earler java database (and another marsupial.
  • Mulgara is entirely community driven, making an open source license ideal.
  • You can read programmer Paul Gearon’s blog to get a good idea of the programming architecture.
  • Mulgara is licensed under the Open Software License v3.0.

So what does Mulgara have to do with PLoS?  Mulgara provides an object database for electronic journals like PLoS ONE and PLoSNTDs to then use other integrated applications (Topaz and  Fedora) to rapidly manipulate and display integrated user-centered journal  features such as annotations, discussions, ratings and tags. Take a look at a typical PLoS ONE article toolbox:

Acyclic Identification of Aptamers for Human alpha-Thrombin Using Over-Represented Libraries and Deep SequencingAdding notes, making comments, and rating the article are making journal reading a communal experience, and open source software applications are being refined and improved from their own communal programming efforts.


Fri, May 20 2011 » Uncategorized

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