临床文本中的不连续命名实体：系统文献综述。

IF 4 2区医学 Q2 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Journal of Biomedical Informatics Pub Date : 2025-02-01 DOI:10.1016/j.jbi.2025.104783

Areej Alhassan , Viktor Schlegel , Monira Aloud , Riza Batista-Navarro , Goran Nenadic

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摘要

本文章由计算机程序翻译，如有差异，请以英文原文为准。

Discontinuous named entities in clinical text: A systematic literature review

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Discontinuous named entities in clinical text: A systematic literature review

Objective

Extracting named entities from clinical free-text presents unique challenges, particularly when dealing with discontinuous entities—mentions that are separated by unrelated words. Traditional NER methods often struggle to accurately identify these entities, prompting the development of specialised computational solutions. This paper systematically reviews and presents the methodologies developed for Discontinuous Named Entity Recognition in clinical texts, highlighting their effectiveness and the challenges they face.

Method

We conducted a systematic literature review focused on discontinuous named entities, using structured searches across four Computer Science-related and one medical-related electronic database. A combination of search terms, grouped into three synonym categories—problem, entity/approach, and task—yielded 2,442 articles. Guided by our research objectives, we identified five key dimensions to systematically annotate and normalise the data for comprehensive analysis.

Result

The review included 44 studies which were coded across several key dimensions: the chronological development of approaches, the corpora used, the downstream tasks affected by discontinuous named entities, the methodological approaches proposed to address the issue, and the reported performance outcomes. The discussion section examines the challenges encountered in this area and suggests potential directions for future research.

Conclusion

Significant progress has been made in discontinuous named entity recognition; however, there remains a need for more adaptable, generalisable solutions that are independent of custom annotation schemes. Exploring various configurations of generative language models presents a promising avenue for advancing this area. Additionally, future research should investigate the impact of precise versus imprecise recognition of discontinuous entities on clinical downstream tasks to better understand its practical implications in healthcare applications.

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来源期刊

Journal of Biomedical Informatics 医学-计算机：跨学科应用

CiteScore

8.90

自引率

6.70%

发文量

243

审稿时长

32 days

期刊介绍： The Journal of Biomedical Informatics reflects a commitment to high-quality original research papers, reviews, and commentaries in the area of biomedical informatics methodology. Although we publish articles motivated by applications in the biomedical sciences (for example, clinical medicine, health care, population health, and translational bioinformatics), the journal emphasizes reports of new methodologies and techniques that have general applicability and that form the basis for the evolving science of biomedical informatics. Articles on medical devices; evaluations of implemented systems (including clinical trials of information technologies); or papers that provide insight into a biological process, a specific disease, or treatment options would generally be more suitable for publication in other venues. Papers on applications of signal processing and image analysis are often more suitable for biomedical engineering journals or other informatics journals, although we do publish papers that emphasize the information management and knowledge representation/modeling issues that arise in the storage and use of biological signals and images. System descriptions are welcome if they illustrate and substantiate the underlying methodology that is the principal focus of the report and an effort is made to address the generalizability and/or range of application of that methodology. Note also that, given the international nature of JBI, papers that deal with specific languages other than English, or with country-specific health systems or approaches, are acceptable for JBI only if they offer generalizable lessons that are relevant to the broad JBI readership, regardless of their country, language, culture, or health system.