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Open Access Highly Accessed Software

Integration of open access literature into the RCSB Protein Data Bank using BioLit

Andreas Prlić1*, Marco A Martinez2, Dimitris Dimitropoulos1, Bojan Beran1, Benjamin T Yukich1, Peter W Rose1, Philip E Bourne12 and J Lynn Fink2*

Author Affiliations

1 San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505 USA

2 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA, 92093-0743 USA

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BMC Bioinformatics 2010, 11:220  doi:10.1186/1471-2105-11-220

Published: 29 April 2010

Abstract

Background

Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB).

Results

BioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. Among other functions, it identifies PDB IDs that are mentioned in the open access literature, by parsing the full text for all research articles in PubMed Central (PMC) and exposing the results as simple XML Web Services. Here, we integrate BioLit results with the RCSB PDB website by using these services to find PDB IDs that are mentioned in research articles and subsequently retrieving abstract, figures, and text excerpts for those articles. A new RCSB PDB literature view permits browsing through the figures and abstracts of the articles that mention a given structure. The BioLit Web Services that are providing the underlying data are publicly accessible. A client library is provided that supports querying these services (Java).

Conclusions

The integration between literature and websites, as demonstrated here with the RCSB PDB, provides a broader view for how a given structure has been analyzed and used. This approach detects the mention of a PDB structure even if it is not formally cited in the paper. Other structures related through the same literature references can also be identified, possibly providing new scientific insight. To our knowledge this is the first time that database and literature have been integrated in this way and it speaks to the opportunities afforded by open and free access to both database and literature content.