title: Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
abstract: Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to large-scale application. In this article, we argue that text-mining technologies have become essential tools in real-world biomedical research. We describe four large scale applications of text mining, as showcased during a recent panel discussion at the BioCreative V Challenge Workshop. We draw on these applications as case studies to characterize common requirements for successfully applying text-mining techniques to practical biocuration needs. We note that system 'accuracy' remains a challenge and identify several additional common difficulties and potential research directions including (i) the 'scalability' issue due to the increasing need of mining information from millions of full-text articles, (ii) the 'interoperability' issue of integrating various text-mining systems into existing curation workflows and (iii) the 'reusability' issue on the difficulty of applying trained systems to text genres that are not seen previously during development. We then describe related efforts within the text-mining community, with a special focus on the BioCreative series of challenge workshops. We believe that focusing on the near-term challenges identified in this work will amplify the opportunities afforded by the continued adoption of text-mining tools. Finally, in order to sustain the curation ecosystem and have text-mining systems adopted for practical benefits, we call for increased collaboration between text-mining researchers and various stakeholders, including researchers, publishers and biocurators.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Ayush
authors.initials: A
authors.lastname: Singhal
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Leaman
authors.affiliation: Selventa, Cambridge, MA 02140, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Catlett
authors.affiliation: EMBO, Meyerhofstrasse 1, Heidelberg 69117, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lemberger
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Johanna
authors.initials: J
authors.lastname: McEntyre
authors.affiliation: Center for Bioinformatics and Computational Biology and Department of Computer and Information Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Polson
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA zhiyong.lu@nih.gov.|Center for Bioinformatics and Computational Biology and Department of Computer and Information Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Arighi
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA zhiyong.lu@nih.gov.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D035843:Biomedical Research; D066289:Data Curation / Q000379:methods*; D057225:Data Mining / Q000379:methods*