Bridging semantics and syntax with graph algorithms state-of-the-art of extracting biomedical relations
Bridging semantics and syntax with graph algorithms state-of-the-art of extracting biomedical relations
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DOI：
10.1093/bib/bbw001
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发表时间：
2017-01-01
影响因子：
9.5
通讯作者：
Szolovits, Peter
中科院分区：
文献类型：
--
作者：
Luo, Yuan;Uzuner, Ozlem;Szolovits, Peter
近年来，生物医学关系提取的研究受到越来越多的关注，在药物基因组学、临床试验筛选、药物不良反应检测等方面有着广泛的生物学和临床应用。准确捕捉表达这些关系的文本中的语义和句法结构的能力对于深入理解科学论文和临床叙述变得越来越重要。生物信息学和临床信息学社区组织了共同的任务挑战，以评估和推进最先进的研究。算法开发和资源建设取得重大进展。特别是，基于图的方法桥接了语义和语法，通常在共享任务中实现最佳性能。然而，在生物医学关系提取的前沿的一些问题继续提出有趣的挑战，并提出了巨大的改进和富有成效的研究的机会。在这篇文章中，我们将生物医学关系提取的背景下，其多功能的应用，提出了一个温和的介绍其一般管道和共享资源，审查目前的国家的最先进的方法进步，讨论的局限性，并指出几个有前途的未来方向。
Research on extracting biomedical relations has received growing attention recently, with numerous biological and clinical applications including those in pharmacogenomics, clinical trial screening and adverse drug reaction detection. The ability to accurately capture both semantic and syntactic structures in text expressing these relations becomes increasingly critical to enable deep understanding of scientific papers and clinical narratives. Shared task challenges have been organized by both bioinformatics and clinical informatics communities to assess and advance the state-of-the-art research. Significant progress has been made in algorithm development and resource construction. In particular, graph-based approaches bridge semantics and syntax, often achieving the best performance in shared tasks. However, a number of problems at the frontiers of biomedical relation extraction continue to pose interesting challenges and present opportunities for great improvement and fruitful research. In this article, we place biomedical relation extraction against the backdrop of its versatile applications, present a gentle introduction to its general pipeline and shared resources, review the current state-of-the-art in methodology advancement, discuss limitations and point out several promising future directions.