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.
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Toward an interactive article: integrating journals and biological databases.

BACKGROUND: Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. RESULTS: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. CONCLUSIONS: Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are