ArticleJournal of the American Medical Informatics Association : JAMIA2022
A scoping review of publicly available language tasks in clinical natural language processing.
Article in Journal of the American Medical Informatics Association : JAMIA, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Use of generative artificial intelligence (AI) in psychiatry and mental health care: a systematic review.Acta neuropsychiatrica · 2024Pooled it
- Comparison of local large language models for extraction of signs and symptoms data from electronic health records.PloS one · 2026Article
- The DRAGON benchmark for clinical NLP.NPJ digital medicine · 2025Article
- Article
- A comparative study of large language model-based zero-shot inference and task-specific supervised classification of breast cancer pathology reports.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- A comparative study of zero-shot inference with large language models and supervised modeling in breast cancer pathology classification.Research square · 2024Article
- ChatGPT, GPT-4, and Other Large Language Models: The Next Revolution for Clinical Microbiology?Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Article
- The shaky foundations of large language models and foundation models for electronic health records.NPJ digital medicine · 2023Review
- Overview of the Problem List Summarization (ProbSum) 2023 Shared Task on Summarizing Patients' Active Diagnoses and Problems from Electronic Health Record Progress Notes.Proceedings of the conference. Association for Computational Linguistics. Meeting · 2023Article
- Progress Note Understanding - Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 shared task.Journal of biomedical informatics · 2023Article
- Deployment of Real-time Natural Language Processing and Deep Learning Clinical Decision Support in the Electronic Health Record: Pipeline Implementation for an Opioid Misuse Screener in Hospitalized Adults.JMIR medical informatics · 2023Article
- DR.BENCH: Diagnostic Reasoning Benchmark for Clinical Natural Language Processing.Journal of biomedical informatics · 2023Article
- Design considerations for a hierarchical semantic compositional framework for medical natural language understanding.PloS one · 2023Article
- Research synthesis as a strategy for advancing biomedical and health informatics knowledge.Journal of the American Medical Informatics Association : JAMIA · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
objectiveTo 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
methodsWe 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.
resultsA 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.
conclusionThe 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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.