This paper is in the following e-collection/theme issue:

Artificial Intelligence (1776) Natural Language Processing (809) Ontologies, Classifications, and Coding (275) Machine Learning (1770) Pathology and Laboratory Medicine (20) Innovations in Cancer Diagnostic and Decision Support (81) Clinical Information and Decision Making (1687)

Published on in Vol 24, No 3 (2022): March

Preprints (earlier versions) of this paper are available at https://preprints.jmir.org/preprint/27210, first published .
A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study

A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study

A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study

Authors of this article:

Joseph Ross Mitchell1, 2, 3 Author Orcid Image ;   Phillip Szepietowski4 Author Orcid Image ;   Rachel Howard4 Author Orcid Image ;   Phillip Reisman4 Author Orcid Image ;   Jennie D Jones4 Author Orcid Image ;   Patricia Lewis4 Author Orcid Image ;   Brooke L Fridley5 Author Orcid Image ;   Dana E Rollison4 Author Orcid Image
Article Authors Cited by (18) Tweetations (9) Metrics

Journals

  1. Sim J, Huang X, Horan M, Baker J, Huang I. Using natural language processing to analyze unstructured patient-reported outcomes data derived from electronic health records for cancer populations: a systematic review. Expert Review of Pharmacoeconomics & Outcomes Research 2024;24(4):467 View
  2. Yang T, Sucholutsky I, Jen K, Schonlau M. exKidneyBERT: a language model for kidney transplant pathology reports and the crucial role of extended vocabularies. PeerJ Computer Science 2024;10:e1888 View
  3. Cheng J. Applications of Large Language Models in Pathology. Bioengineering 2024;11(4):342 View
  4. Zheng Y, Cai Y, Yan Y, Chen S, Gong K. Novel Approach to Personalized Physician Recommendations Using Semantic Features and Response Metrics: Model Evaluation Study. JMIR Human Factors 2024;11:e57670 View
  5. Cho H, Jun T, Kim Y, Kang H, Ahn I, Gwon H, Kim Y, Seo J, Choi H, Kim M, Han J, Kee G, Park S, Ko S. Task-Specific Transformer-Based Language Models in Health Care: Scoping Review. JMIR Medical Informatics 2024;12:e49724 View
  6. Ameli N, Firoozi T, Gibson M, Lai H, Cheungpasitporn W. Classification of periodontitis stage and grade using natural language processing techniques. PLOS Digital Health 2024;3(12):e0000692 View
  7. Zitu M, Le T, Duong T, Haddadan S, Garcia M, Amorrortu R, Zhao Y, Rollison D, Thieu T. Large language models in cancer: potentials, risks, and safeguards. BJR|Artificial Intelligence 2025;2(1) View
  8. Hurtado L, Marco-Ruiz L, Segarra E, Castro-Bleda M, Bustos-Moreno A, Iglesia-Vayá M, Vallalta-Rueda J. Leveraging Transformers-based models and linked data for deep phenotyping in radiology. Computer Methods and Programs in Biomedicine 2025;260:108567 View
  9. Chen Y, Zhang C, Bai R, Sun T, Ding W, Wang R. A review of medical text analysis: Theory and practice. Information Fusion 2025;119:103024 View
  10. Park P, Choi Y, Han N, Park Y, Hwang J, Chae H, Yoo C, Choi K, Kim H, Consoli S. Leveraging natural language processing for efficient information extraction from breast cancer pathology reports: Single-institution study. PLOS ONE 2025;20(2):e0318726 View
  11. Chen D, Alnassar S, Avison K, Huang R, Raman S. Large Language Model Applications for Health Information Extraction in Oncology: Scoping Review. JMIR Cancer 2025;11:e65984 View
  12. Lee D, Vaid A, Menon K, Freeman R, Matteson D, Marin M, Nadkarni G. Using Large Language Models to Automate Data Extraction From Surgical Pathology Reports: Retrospective Cohort Study. JMIR Formative Research 2025;9:e64544 View
  13. Oyewusi W, Vasquez Osorio E, Nenadic G, MacGregor I, Price G. Data, dialogue, and design: patient and public involvement and engagement for natural language processing with real-world cancer data. Frontiers in Digital Health 2025;7 View
  14. Dai J, Kim M, Sutton R, Mitchell J, Goebel R, Baumgart D. Comparative analysis of natural language processing methodologies for classifying computed tomography enterography reports in Crohn’s disease patients. npj Digital Medicine 2025;8(1) View

Conference Proceedings

  1. Li M, Li H. 2022 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology (WI-IAT). Research on Question Answering over Knowledge Graph of Chronic Diseases View
  2. Tiwari S, Goyal H, adnan M, Shrivastava A, Yadav K, Rao A. 2024 International Conference on Communication, Computer Sciences and Engineering (IC3SE). Clinical Text Analysis with Natural Language Processing: A BERT-based Approach View
  3. Ouchene H, Mezzi M, Oukid L, Benblidia N, Bentayeb F. 2024 IEEE/ACS 21st International Conference on Computer Systems and Applications (AICCSA). Classification of Cancer Pathology Reports Using Rule-Based Approaches: A Review View
  4. Duong T, Thieu T. 2024 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI). OncoNLP: Cancer Comprehend Annotation - a Pipeline for Cancer Phenotype and Clinical Extraction View