A scoping review of publicly available language tasks in clinical natural language processing

Gao, YJ (通讯作者),Univ Wisconsin, Sch Med & Publ Hlth, ICU Data Sci Lab, Madison, WI 53706 USA.
2022-9-12
Objective To provide a scoping review of papers on clinical natural language processing (NLP) shared tasks that use publicly available electronic health record data from a cohort of patients. Materials and Methods We searched 6 databases, including biomedical research and computer science literature databases. A round of title/abstract screening and full-text screening were conducted by 2 reviewers. Our method followed the PRISMA-ScR guidelines. Results A total of 35 papers with 48 clinical NLP tasks met inclusion criteria between 2007 and 2021. We categorized the tasks by the type of NLP problems, including named entity recognition, summarization, and other NLP tasks. Some tasks were introduced as potential clinical decision support applications, such as substance abuse detection, and phenotyping. We summarized the tasks by publication venue and dataset type. Discussion The breadth of clinical NLP tasks continues to grow as the field of NLP evolves with advancements in language systems. However, gaps exist with divergent interests between the general domain NLP community and the clinical informatics community for task motivation and design, and in generalizability of the data sources. We also identified issues in data preparation. Conclusion The existing clinical NLP tasks cover a wide range of topics and the field is expected to grow and attract more attention from both general domain NLP and clinical informatics community. We encourage future work to incorporate multidisciplinary collaboration, reporting transparency, and standardization in data preparation. We provide a listing of all the shared task papers and datasets from this review in a GitLab repository.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
卷号:29|期号:10|页码:1797-1806
ISSN:1067-5027|收录类别:SCIE
语种
英语
来源机构
University of Wisconsin System; University of Wisconsin Madison; Loyola University Chicago; University of Wisconsin System; University of Wisconsin Madison; Harvard University; Boston Children's Hospital; George Mason University
资助信息
This work was supported by NIH/NIDA grant number R01DA051464 (to MA), NIH/NIGM grant number R01 HL157262 (to MMC), NIH/NLM grant numbers R01LM012973 and R01LM012918 (to TIM), NIH NLM grant number R01LM010090 (to TM and DD), and NIH/NLM grant number R13LM013127 (to OU).
被引频次(WOS)
1
被引频次(其他)
1
180天使用计数
4
2013以来使用计数
5
EISSN
1527-974X
出版年
2022-9-12
DOI
10.1093/jamia/ocac127
学科领域
循证公共卫生
关键词
natural language processing clinical informatics electronic health records systematic review clinical decision support
资助机构
NIH/NIDA(United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute on Drug Abuse (NIDA)) NIH/NIGM(United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA) NIH/NLM(United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Library of Medicine (NLM)) NIH NLM(United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Library of Medicine (NLM))
WOS学科分类
Computer Science, Information Systems Computer Science, Interdisciplinary Applications Health Care Sciences & Services Information Science & Library Science Medical Informatics