期刊
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
卷 -, 期 -, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/database/baw161
关键词
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资金
- National Institutes of Health [R13-GM109648-01A1, P20-GM103446]
- Intramural Research Program at National Library of Medicine
- US Department of Energy [DE-SC0010838]
- US National Science Foundation [DBI-1356374]
- Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI)
- SyBIT project of the SystemsX.ch
- Swiss Initiative in Systems Biology
- Robert Bosch Foundation
- EMBO
- Wellcome Grant, UK PubMed Central Phase 3 Developments [098231/Z/12/Z]
- Wellcome Trust [098231/Z/12/Z] Funding Source: Wellcome Trust
- U.S. Department of Energy (DOE) [DE-SC0010838] Funding Source: U.S. Department of Energy (DOE)
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.
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