Extracting cancer concepts from clinical notes using natural language processing: a systematic review

BMC Bioinformatics

Research

Leila Ahmadian¹  Reza Khajouei¹  Sadrieh Hajesmaeel Gohari²  Maryam Gholipour³  Parastoo Amiri³ 

[1] Department of Health Information Sciences, Faculty of Management and Medical Information Sciences, Kerman University of Medical Sciences, Kerman, Iran;Medical Informatics Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran;Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran;

关键词: Neoplasms;    Natural language processing;    NLP;    Machine learning;    Terminology;    Information system;    Systematic review;   

DOI  :  10.1186/s12859-023-05480-0

 received in 2022-12-13, accepted in 2023-09-13,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundExtracting information from free texts using natural language processing (NLP) can save time and reduce the hassle of manually extracting large quantities of data from incredibly complex clinical notes of cancer patients. This study aimed to systematically review studies that used NLP methods to identify cancer concepts from clinical notes automatically.MethodsPubMed, Scopus, Web of Science, and Embase were searched for English language papers using a combination of the terms concerning “Cancer”, “NLP”, “Coding”, and “Registries” until June 29, 2021. Two reviewers independently assessed the eligibility of papers for inclusion in the review.ResultsMost of the software programs used for concept extraction reported were developed by the researchers (n = 7). Rule-based algorithms were the most frequently used algorithms for developing these programs. In most articles, the criteria of accuracy (n = 14) and sensitivity (n = 12) were used to evaluate the algorithms. In addition, Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT) and Unified Medical Language System (UMLS) were the most commonly used terminologies to identify concepts. Most studies focused on breast cancer (n = 4, 19%) and lung cancer (n = 4, 19%).ConclusionThe use of NLP for extracting the concepts and symptoms of cancer has increased in recent years. The rule-based algorithms are well-liked algorithms by developers. Due to these algorithms' high accuracy and sensitivity in identifying and extracting cancer concepts, we suggested that future studies use these algorithms to extract the concepts of other diseases as well.

【 授权许可】

CC BY   
© The Author(s) 2023

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