Abstract
Biomedical text mining promises to assist biologists in quickly navigating the combined knowledge in their domain. This would allow improved understanding of the complex interactions within biological systems and faster hypothesis generation. New biomedical research articles are published daily and text mining tools are only as good as the corpus from which they work. Many text mining tools are underused because their results are static and do not reflect the constantly expanding knowledge in the field. In order for biomedical text mining to become an indispensable tool used by researchers, this problem must be addressed. To this end, we present PubRunner, a framework for regularly running text mining tools on the latest publications. PubRunner is lightweight, simple to use, and can be integrated with an existing text mining tool. The workflow involves downloading the latest abstracts from PubMed, executing a user-defined tool, pushing the resulting data to a public FTP, and publicizing the location of these results on the public PubRunner website. This shows a proof of concept that we hope will encourage text mining developers to build tools that truly will aid biologists in exploring the latest publications.
Highlights
The National Library of Medicine’s (NLM) PubMed database contains over 27 million citations and is growing exponentially (Lu, 2011)
In order to encourage biomedical text mining researchers to widely share their results and code, and keep analyses up-to-date, we present PubRunner
A central website was developed to track the status of different text mining analyses that are managed by PubRunner
Summary
3. Julien Gobeill, University of Applied Sciences and Arts of Western Switzerland (HES-SO, HEG (Geneva School of Management)), Carouge, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland. This article is included in the Container Virtualization in Bioinformatics collection. This article is included in the Hackathons collection. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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