Clinical natural language processing for secondary uses

doi:10.1016/j.jbi.2024.104596

Editorial

. 2024 Feb:150:104596.

doi: 10.1016/j.jbi.2024.104596. Epub 2024 Jan 24.

Clinical natural language processing for secondary uses

Yanjun Gao¹, Diwakar Mahajan², Özlem Uzuner³, Meliha Yetisgen⁴

Affiliations

¹ Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States. Electronic address: ygao@medicine.wisc.edu.
² Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States. Electronic address: https://twitter.com/diwakarmahajan.
³ Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States. Electronic address: https://twitter.com/ozlem_uzuner_gm.
⁴ Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States.

PMID: 38278312
PMCID: PMC11212507
DOI: 10.1016/j.jbi.2024.104596

Editorial

Clinical natural language processing for secondary uses

Yanjun Gao et al. J Biomed Inform. 2024 Feb.

. 2024 Feb:150:104596.

doi: 10.1016/j.jbi.2024.104596. Epub 2024 Jan 24.

Authors

Yanjun Gao¹, Diwakar Mahajan², Özlem Uzuner³, Meliha Yetisgen⁴

Affiliations

¹ Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States. Electronic address: ygao@medicine.wisc.edu.
² Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States. Electronic address: https://twitter.com/diwakarmahajan.
³ Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States. Electronic address: https://twitter.com/ozlem_uzuner_gm.
⁴ Department of Medicine, University of Wisconsin Madison, Madison, WI, United States; IBM T.J. Watson Research Center, Yorktown Heights, NY, United States; Department of Information Sciences and Technology, George Mason University, Fairfax, VA, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, United States.

PMID: 38278312
PMCID: PMC11212507
DOI: 10.1016/j.jbi.2024.104596

No abstract available

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Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Adapting Generative Large Language Models for Information Extraction from Unstructured Electronic Health Records in Residential Aged Care: A Comparative Analysis of Training Approaches.
Vithanage D, Deng C, Wang L, Yin M, Alkhalaf M, Zhang Z, Zhu Y, Yu P. Vithanage D, et al. J Healthc Inform Res. 2025 Feb 20;9(2):191-219. doi: 10.1007/s41666-025-00190-z. eCollection 2025 Jun. J Healthc Inform Res. 2025. PMID: 40309133 Free PMC article.

References

1. Mahajan D, Liang JJ, Tsou C-H, Uzuner Ö, Overview of the 2022 n2c2 shared task on contextualized medication event extraction in clinical notes, J. Biomed. Inform (2023) 104432. - PMC - PubMed
1. Tsujimura T, Yamada K, Ida R, Miwa M, Sasaki Y, Contextualized medication event extraction with striding NER and multi-turn QA, J. Biomed. Inf 144 (2023) 104416, 10.1016/j.jbi.2023.104416 [published Online First: Epub Date]. - DOI - PubMed
1. Vasilakes J, Georgiadis P, Nguyen NTH, Miwa M, Ananiadou S, Contextualized medication event extraction with levitated markers, J. Biomed. Inf 141 (2023) 104347, 10.1016/j.jbi.2023.104347 [published Online First: Epub Date]. - DOI - PubMed
1. Chen A, Yu Z, Yang X, Guo Y, Bian J, Wu Y, Contextualized medication information extraction using transformer-based deep learning architectures, J. Biomed. Inf 142 (2023) 104370, 10.1016/j.jbi.2023.104370 [published Online First: Epub Date]. - DOI - PMC - PubMed
1. Gan Q, Hu M, Peterson KS, et al., A deep learning approach for medication disposition and corresponding attributes extraction, J. Biomed. Inf 143 (2023) 104391, 10.1016/j.jbi.2023.104391 [published Online First: Epub Date]. - DOI - PMC - PubMed

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[1] Mahajan D, Liang JJ, Tsou C-H, Uzuner Ö, Overview of the 2022 n2c2 shared task on contextualized medication event extraction in clinical notes, J. Biomed. Inform (2023) 104432. - PMC - PubMed

[2] Mahajan D, Liang JJ, Tsou C-H, Uzuner Ö, Overview of the 2022 n2c2 shared task on contextualized medication event extraction in clinical notes, J. Biomed. Inform (2023) 104432. - PMC - PubMed

[3] Tsujimura T, Yamada K, Ida R, Miwa M, Sasaki Y, Contextualized medication event extraction with striding NER and multi-turn QA, J. Biomed. Inf 144 (2023) 104416, 10.1016/j.jbi.2023.104416 [published Online First: Epub Date]. - DOI - PubMed

[4] Tsujimura T, Yamada K, Ida R, Miwa M, Sasaki Y, Contextualized medication event extraction with striding NER and multi-turn QA, J. Biomed. Inf 144 (2023) 104416, 10.1016/j.jbi.2023.104416 [published Online First: Epub Date]. - DOI - PubMed

[5] Vasilakes J, Georgiadis P, Nguyen NTH, Miwa M, Ananiadou S, Contextualized medication event extraction with levitated markers, J. Biomed. Inf 141 (2023) 104347, 10.1016/j.jbi.2023.104347 [published Online First: Epub Date]. - DOI - PubMed

[6] Vasilakes J, Georgiadis P, Nguyen NTH, Miwa M, Ananiadou S, Contextualized medication event extraction with levitated markers, J. Biomed. Inf 141 (2023) 104347, 10.1016/j.jbi.2023.104347 [published Online First: Epub Date]. - DOI - PubMed

[7] Chen A, Yu Z, Yang X, Guo Y, Bian J, Wu Y, Contextualized medication information extraction using transformer-based deep learning architectures, J. Biomed. Inf 142 (2023) 104370, 10.1016/j.jbi.2023.104370 [published Online First: Epub Date]. - DOI - PMC - PubMed

[8] Chen A, Yu Z, Yang X, Guo Y, Bian J, Wu Y, Contextualized medication information extraction using transformer-based deep learning architectures, J. Biomed. Inf 142 (2023) 104370, 10.1016/j.jbi.2023.104370 [published Online First: Epub Date]. - DOI - PMC - PubMed

[9] Gan Q, Hu M, Peterson KS, et al., A deep learning approach for medication disposition and corresponding attributes extraction, J. Biomed. Inf 143 (2023) 104391, 10.1016/j.jbi.2023.104391 [published Online First: Epub Date]. - DOI - PMC - PubMed

[10] Gan Q, Hu M, Peterson KS, et al., A deep learning approach for medication disposition and corresponding attributes extraction, J. Biomed. Inf 143 (2023) 104391, 10.1016/j.jbi.2023.104391 [published Online First: Epub Date]. - DOI - PMC - PubMed

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Clinical natural language processing for secondary uses

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Clinical natural language processing for secondary uses

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