Publishing Interactive Articles: Integrating Journals And Biological Databases

In collaboration with the journal GENETICS, we've developed and launched a pipeline by which interactive full-text HTML/PDF journal articles are published with named entities linked to corresponding resource pages in "WormBase":http://www.wormbase.org/ (WB). Our interactive articles allow a reader to click on over ten different data type objects (gene, protein, transgene, etc.) and be directed to the relevant webpage. This seamless connection from the article to summaries of data types promotes a deeper level of understanding for the naïve reader, and incisive evaluation for the sophisticated reader. Further, this collaboration allows us to identify and collect information before the publication of the article. The pipeline uses automated recognition scripts to identify entities that already exist in the database and a self-reporting form we created at WB that is sent to the author by GENETICS for submitting entities that do not already exist in our database. We include a manual quality control step to make sure ambiguous links are corrected, and that all new entities have been reported and linked properly. The automated entity recognition scripts allows us to potentially link any object found in a database as well as to expand this pipeline to other databases. We have already adapted this pipeline for linking Saccharomyces cerevisiae GENETICS articles to the "Saccharomyces Genome Database":http://www.yeastgenome.org/ (SGD) and are currently expanding this pipeline for linking genes in Drosophila articles to "FlyBase":http://flybase.org/. By integrating journals and databases, we are integrating the major modes of communication in the biological sciences, which will undoubtedly increase the pace of discovery.