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. 2008 Jul 1;36(Web Server issue):W385-9.
doi: 10.1093/nar/gkn317. Epub 2008 May 31.

BioLit: integrating biological literature with databases

J Lynn Fink  1 , Sergey Kushch, Parker R Williams, Philip E Bourne
Affiliations

BioLit: integrating biological literature with databases

J Lynn Fink et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1.
Figure 1.
A screenshot of the BioLit article viewer. This customized viewer not only displays the full text of an article as it was originally published but also displays integrated metadata from the BioLit database. PDB IDs can be seen highlighted in yellow and Gene Ontology terms are highlighted in lavender. Clicking on a highlighted terms brings up information, a list of options or links associated with each term. Article shown is in PLoS Comput. Biol., 2006, 2, e90.
Figure 2.
Figure 2.
Entry from the BioLit PDB clone that has citations inthe BioLit database.
See this image and copyright information in PMC

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