Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

• DOI: 10.1093/database/baw161
• Publication Date: 2016-11-16T15:05:49Z
• Authors: Ayush Singhal; Robert Leaman; Natalie Catlett; Thomas Lemberger; Johanna McEntyre; Shawn Polson; Ioannis Xenarios; Cecilia Arighi; Zhiyong Lu
• Keywords: Biomedical text mining

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 real-world research. We describe four large scale applications of text mining, as showcased during a recent panel discussion at BioCreative V Challenge Workshop. draw on these case studies characterize common requirements for successfully applying techniques practical biocuration needs. note system 'accuracy' remains challenge and identify several additional difficulties potential research directions including (i) 'scalability' issue due increasing need information millions full-text articles, (ii) 'interoperability' integrating various systems into existing curation workflows (iii) 'reusability' difficulty trained genres are not seen previously development. then related efforts within community, with special focus series workshops. believe focusing near-term challenges identified work will amplify opportunities afforded by continued adoption tools. Finally, order sustain ecosystem adopted benefits, call increased collaboration between researchers stakeholders, researchers, publishers biocurators.