One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

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Lars Juhl Jensen

Science

open source
bitbucket.org/larsjuhljensen/tagger/

Docker
hub.docker.com/r/larsjuhljensen/tagger/

Jensen et al., Nature Reviews Genetics, 2012

Drug introduction Drug discontinuation
Adverse eventNegative modifier Indication Pre-existing
condition
Adverse drug reaction Possible
adverse drug reaction
Adverse event
ADR of
additional drug
Identification start
Eriksson et al., Drug Safety, 2014

Acknowledgments
Evangelos Pafilis
Sune Pletscher-
Frankild
Nadezhda
Doncheva
Damian Szklarczyk
Michael Kuhn
Robert Eriksson
John “Scooter”
Morris
Tudor Oprea
Christian von
Mering
Peer Bork
Christos Arvanitidis
Søren Brunak

One tagger, many uses: Illustrating the power of dictionary-based named entity recognition

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Abstract Technology has significantly changed how research is done in biology. Along with this shift, it is increasingly easier and advantageous to operate in an open science framework. In this presentation I will begin by providing an overview of our research efforts with particularly attention to challenges in data analysis. Research in our lab focuses on characterizing physiological responses of shellfish to environmental change, examining impacts and adaptive potential from the nucleotide to organism level. A core component of this includes investigating the functional relationship of genetics, epigenetics, and transcription. In our research we leverage several computing infrastructure solutions that I will describe. In addition, our lab practices Open Notebook Science. I will describe the practical aspects of how we accomplish this including addressing some of the concerns and realized advantages. Beyond online lab notebooks, we are continually experimenting with different ways to use online resources to engage with a larger audience and improve science communication. I have found this is a complex balance of time and effort versus impact and will discuss how our lab group attempts to reach this balance. Bio Steven Roberts is an Associate Professor in the School of Aquatic and Fishery Sciences where his research centers around characterizing the response of aquatic organisms to environmental change. Prior to coming to the University of Washington, in 2007 he was at the Marine Biological Laboratory in Woods Hole, Massachusetts and received his PhD from the University of Notre Dame. In graduate school he spent most of his time transferring agarose gels, and now he spends most of his time transferring files.

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