论文标题
COVID-19符号:通用临床NLP工具的快速适应,以识别和使COVID-19的标志和症状归一化为OMOP公共数据模型
COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model
论文作者
论文摘要
19009年的大流行迅速席卷了世界,感染了数百万人。一种有效的工具,可以准确地识别电子健康记录(EHR)中自由文本的重要临床概念,对于加速COVID-19临床研究非常有价值。为此,这项研究旨在调整现有的夹具自然语言处理工具来快速构建Covid-19标志,该工具可以从临床文本中提取Covid-19符号及其8个符号/症状及其8个属性及其8个属性(身体位置,严重性,时间表,时间表,病情,状况,不确定性,否定和过程)。提取的信息还映射到观察性医学结果伙伴关系公共数据模型中的标准概念。采用了将基于深度学习的模型,精选词典和基于模式的规则结合的混合方法,以快速从夹具中构建COVID-19标志,并具有优化的性能。我们使用3个外部站点进行了广泛的评估,其中包含COVID-19患者的临床注释,以及Covid-19的在线医疗对话,表明Covid-19 sign-Sym可以在数据源中实现高性能。本研究使用的工作流程可以推广到其他用例,在短时间内需要根据特定信息需求对现有的临床自然语言处理工具进行定制。研究社区可以自由访问Covid-19的标志(https://clamp.uth.uth.edu/covid/nlp.php),并已被16个医疗保健组织用于支持Covid-19的临床研究。
The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.