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Nucleic Acids Research Advance Access originally published online on May 31, 2008
Nucleic Acids Research 2008 36(Web Server issue):W385-W389; doi:10.1093/nar/gkn317
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W385-W389
© 2008 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.

Articles

BioLit: integrating biological literature with databases

J. Lynn Fink*, Sergey Kushch, Parker R. Williams and Philip E. Bourne

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, 92093-0444, USA

*To whom correspondence should be addressed. Tel: +1 858 822 1897; Fax: + 1 858 822 3610; Email: jlfink{at}ucsd.edu

Received January 30, 2008. Revised April 22, 2008. Accepted May 7, 2008.

BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed Central. Specifically, these metadata include database identifiers and ontology terms found within the full text of the article. BioLit delivers these metadata in the form of XML-based article files and as a custom web-based article viewer that provides context-specific functionality to the metadata. This resource aims to integrate the traditional scientific publication directly into existing biological databases, thus obviating the need for a user to search in multiple locations for information relating to a specific item of interest, for example published experimental results associated with a particular biological database entry. As an example of a possible use of BioLit, we also present an instance of the Protein Data Bank fully integrated with BioLit data. We expect that the community of life scientists in general will be the primary end-users of the web-based viewer, while biocurators will make use of the metadata-containing XML files and the BioLit database of article data. BioLit is available at http://biolit.ucsd.edu.


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