BioLit: integrating biological literature with databases

@article{citeulike:2853948, 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. 10.1093/nar/gkn317}, author = {Fink, Lynn J. and Kushch, Sergey and Williams, Parker R. and Bourne, Philip E. }, citeulike-article-id = {2853948}, doi = {http://dx.doi.org/10.1093/nar/gkn317}, journal = {Nucl. Acids Res.}, keywords = {database, literature, metadata, semantic, webserver}, month = {May}, pages = {gkn317+}, posted-at = {2008-06-01 07:09:31}, priority = {2}, title = {BioLit: integrating biological literature with databases}, url = {http://dx.doi.org/10.1093/nar/gkn317}, year = {2008} }

TY - JOUR ID - citeulike:2853948 L3 - citeulike-article-id:2853948 TI - BioLit: integrating biological literature with databases JF - Nucl. Acids Res. SP - gkn317 N2 - 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. 10.1093/nar/gkn317 KW - database KW - literature KW - metadata KW - semantic KW - webserver AU - Fink, Lynn AU - Kushch, Sergey AU - Williams, Parker AU - Bourne, Philip PY - 2008/05/31/ UR - http://dx.doi.org/10.1093/nar/gkn317 ER -