28 Jan 2007

Mashups, mirrors, mining and open access

The Creative Commons Attribution License under which open access articles are made available by both BioMed Central and PLoS allows others to create sites that incorporate the content of these articles, so long as the original source is clearly acknowledged.

Two ways to do this are mashups and mirrors. According to Wikipedia, a mashup is a site that "combines content from more than one source into an integrated experience". A mirror is an exact copy of a website.

BioMed Central officially has four mirrors to which we feed content, at INIST in France, University of Potsdam in Germany, PubMed Central at the NIH, and the National Library of the Netherlands' e-Depot. I've come across some unofficial mirrors in specific areas like genomics and bioinformatics in the past.

PLoS ONE already has its own unofficial mirror, created by the people behind HubMed: PLoS Too. Rather than displaying the articles as they appear on the publisher's site, this is a pared-down view of the articles and it has a couple of good new features - auto-generated tags for each article, and a very quick live search box.

On the mashup side, Free Biomedical Images has made open access images available in a searchable database, mainly (entirely?) taken from BioMed Central articles, and fully attributed. Users can comment on the images, rate them, email them to a friend and jump to the published article.

A key feature of open access is that we don't hide away the full text of our articles. The entire 'corpus' of our open access research articles is available on our data mining page for anyone to download. Gerry Rubin has said that "the most important reason for Open Access is data mining".

The idea of mashups, scripts and extensions is just beginning to reach the bioinformatics community. A bioinformatics mashup by Alfonso Valencia is iHOP (Information Hyperlinked over Proteins), which links information about genes and proteins to text from PubMed. Not satisfied with just a mashup, Mark Wilkinson has created a Greasemonkey userscript called iHOPerator that enhances the iHOP website with tag clouds. You can read about in his BMC Bioinformatics article. Two other Greasemonkey userscripts link PubMed to social bookmarking sites, one to CiteULike, the other to Connotea. A third links Google Scholar to CiteULike. The iSpecies search engine pulls together information about any species you enter from disparate sources, including scores of biomedical databases and even Yahoo! Image search.

Mashups, mirrors and mining are definitely the future of science publishing.


thomas.nicolai said...

Another mashup service across OA journals and institutions: http://www.scientificcommons.org

Matt Hodgkinson said...

This post was cited in John Willinsky, Sally Murray, Claire Kendall, Anita Palepu. Doing Medical Journals Differently:
Open Medicine, Open Access,
and Academic Freedom
. Canadian Journal of Communication 2007, 32:3