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Bioinformatics Advance Access originally published online on March 28, 2007
Bioinformatics 2007 23(11):1434-1436; doi:10.1093/bioinformatics/btm109
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

uBioRSS: Tracking taxonomic literature using RSS

Patrick R. Leary 1, David P. Remsen 2, Catherine N. Norton 1, David J. Patterson 1 and Indra Neil Sarkar 1,*

1MBL Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA and 2Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen, Denmark

*To whom correspondence should be addressed.


  Abstract

Summary: Web content syndication through standard formats such as RSS and ATOM has become an increasingly popular mechanism for publishers, news sources and blogs to disseminate regularly updated content. These standardized syndication formats deliver content directly to the subscriber, allowing them to locally aggregate content from a variety of sources instead of having to find the information on multiple websites. The uBioRSS application is a ‘taxonomically intelligent’ service customized for the biological sciences. It aggregates syndicated content from academic publishers and science news feeds, and then uses a taxonomic Named Entity Recognition algorithm to identify and index taxonomic names within those data streams. The resulting name index is cross-referenced to current global taxonomic datasets to provide context for browsing the publications by taxonomic group. This process, called taxonomic indexing, draws upon services developed specifically for biological sciences, collectively referred to as ‘taxonomic intelligence’. Such value-added enhancements can provide biologists with accelerated and improved access to current biological content.

Availability: http://names.ubio.org/rss/

Contact: sarkar{at}mbl.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dr. Jonathan Wren

Received on February 2, 2007; revised on March 13, 2007; accepted on March 13, 2007

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