BioLit: integrating biological literature with databases

J. L. Fink, S. Kushch, P. R. Williams, P. E. Bourne
2008 Nucleic Acids Research  
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
more » ... ta. 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 webbased 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.
doi:10.1093/nar/gkn317 pmid:18515836 pmcid:PMC2447735 fatcat:d2utaoxvzzaovelv3e6oqpswx4