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dc.contributor.authorAnekalla, K.R.
dc.contributor.authorCourneya, J.P.
dc.contributor.authorFiorini, N.
dc.date.accessioned2019-11-01T12:49:40Z
dc.date.available2019-11-01T12:49:40Z
dc.date.issued2017
dc.identifier.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85037693042&doi=10.12688%2ff1000research.11389.1&partnerID=40&md5=20d63e121e7b6c75e3d1b02cfe301d97
dc.identifier.urihttp://hdl.handle.net/10713/11355
dc.description.abstractBiomedical 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. Copyright 2017 Anekalla KR et al.en_US
dc.description.sponsorshipThis research was supported by the Intramural Research Program of the NIH, National Library of Medicine. JL is supported by a Vanier Canada Graduate Scholarship.en_US
dc.description.urihttps://doi.org/10.12688/f1000research.11389.1en_US
dc.language.isoen_USen_US
dc.publisherFaculty of 1000 Ltden_US
dc.relation.ispartofF1000Research
dc.titlePubRunner: A light-weight framework for updating text mining resultsen_US
dc.typeArticleen_US
dc.identifier.doi10.12688/f1000research.11389.1


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