TY - JOUR
T1 - Clinical information extraction applications
T2 - A literature review
AU - Wang, Yanshan
AU - Wang, Liwei
AU - Rastegar-Mojarad, Majid
AU - Moon, Sungrim
AU - Shen, Feichen
AU - Afzal, Naveed
AU - Liu, Sijia
AU - Zeng, Yuqun
AU - Mehrabi, Saeed
AU - Sohn, Sunghwan
AU - Liu, Hongfang
N1 - Publisher Copyright:
© 2017 The Authors
PY - 2018/1
Y1 - 2018/1
N2 - Background With the rapid adoption of electronic health records (EHRs), it is desirable to harvest information and knowledge from EHRs to support automated systems at the point of care and to enable secondary use of EHRs for clinical and translational research. One critical component used to facilitate the secondary use of EHR data is the information extraction (IE) task, which automatically extracts and encodes clinical information from text. Objectives In this literature review, we present a review of recent published research on clinical information extraction (IE) applications. Methods A literature search was conducted for articles published from January 2009 to September 2016 based on Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and ACM Digital Library. Results A total of 1917 publications were identified for title and abstract screening. Of these publications, 263 articles were selected and discussed in this review in terms of publication venues and data sources, clinical IE tools, methods, and applications in the areas of disease- and drug-related studies, and clinical workflow optimizations. Conclusions Clinical IE has been used for a wide range of applications, however, there is a considerable gap between clinical studies using EHR data and studies using clinical IE. This study enabled us to gain a more concrete understanding of the gap and to provide potential solutions to bridge this gap.
AB - Background With the rapid adoption of electronic health records (EHRs), it is desirable to harvest information and knowledge from EHRs to support automated systems at the point of care and to enable secondary use of EHRs for clinical and translational research. One critical component used to facilitate the secondary use of EHR data is the information extraction (IE) task, which automatically extracts and encodes clinical information from text. Objectives In this literature review, we present a review of recent published research on clinical information extraction (IE) applications. Methods A literature search was conducted for articles published from January 2009 to September 2016 based on Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and ACM Digital Library. Results A total of 1917 publications were identified for title and abstract screening. Of these publications, 263 articles were selected and discussed in this review in terms of publication venues and data sources, clinical IE tools, methods, and applications in the areas of disease- and drug-related studies, and clinical workflow optimizations. Conclusions Clinical IE has been used for a wide range of applications, however, there is a considerable gap between clinical studies using EHR data and studies using clinical IE. This study enabled us to gain a more concrete understanding of the gap and to provide potential solutions to bridge this gap.
KW - Application
KW - Clinical notes
KW - Electronic health records
KW - Information extraction
KW - Natural language processing
UR - http://www.scopus.com/inward/record.url?scp=85036479720&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85036479720&partnerID=8YFLogxK
U2 - 10.1016/j.jbi.2017.11.011
DO - 10.1016/j.jbi.2017.11.011
M3 - Review article
C2 - 29162496
AN - SCOPUS:85036479720
SN - 1532-0464
VL - 77
SP - 34
EP - 49
JO - Journal of Biomedical Informatics
JF - Journal of Biomedical Informatics
ER -