• Wei Yu, Chengyi Zheng, Fagen Xie, Wansu Chen, Cheryl Mercado, Lina S Sy, Lei Qian, Sungching Glenn, Hung F Tseng, Gina Lee, Jonathan Duffy, Michael M McNeil, Matthew F Daley, Brad Crane, Huong Q McLean, Lisa A Jackson, and Steven J Jacobsen.
• Kaiser Permanente Southern California, Pasadena, CA, USA.
• Pharmacoepidemiol Drug Saf. 2020 Feb 1; 29 (2): 182-188.

PurposeThe objective was to develop a natural language processing (NLP) algorithm to identify vaccine-related anaphylaxis from plain-text clinical notes, and to implement the algorithm at five health care systems in the Vaccine Safety Datalink.MethodsThe NLP algorithm was developed using an internal NLP tool and training dataset of 311 potential anaphylaxis cases from Kaiser Permanente Southern California (KPSC). We applied the algorithm to the notes of another 731 potential cases (423 from KPSC; 308 from other sites) with relevant codes (ICD-9-CM diagnosis codes for anaphylaxis, vaccine adverse reactions, and allergic reactions; Healthcare Common Procedure Coding System codes for epinephrine administration). NLP results were compared against a reference standard of chart reviewed and adjudicated cases. The algorithm was then separately applied to the notes of 6 427 359 KPSC vaccination visits (9 402 194 vaccine doses) without relevant codes.ResultsAt KPSC, NLP identified 12 of 16 true vaccine-related cases and achieved a sensitivity of 75.0%, specificity of 98.5%, positive predictive value (PPV) of 66.7%, and negative predictive value of 99.0% when applied to notes of patients with relevant diagnosis codes. NLP did not identify the five true cases at other sites. When NLP was applied to the notes of KPSC patients without relevant codes, it captured eight additional true cases confirmed by chart review and adjudication.ConclusionsThe current study demonstrated the potential to apply rule-based NLP algorithms to clinical notes to identify anaphylaxis cases. Increasing the size of training data, including clinical notes from all participating study sites in the training data, and preprocessing the clinical notes to handle special characters could improve the performance of the NLP algorithms. We recommend adding an NLP process followed by manual chart review in future vaccine safety studies to improve sensitivity and efficiency.© 2019 John Wiley & Sons, Ltd.

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