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Pharmacoepidemiol Drug Saf. 2019 Dec 3. doi: 10.1002/pds.4919. [Epub ahead of print]

The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink.

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Kaiser Permanente Southern California, Pasadena, CA, USA.
Centers for Disease Control and Prevention, Atlanta, GA, USA.
Kaiser Permanente Colorado, Denver, CO, USA.
Kaiser Permanente Northwest, Portland, OR, USA.
Marshfield Clinic Research Institute, Marshfield, WI, USA.
Kaiser Permanente Washington Health Research Institute (previously Group Health Research Institute), Seattle, WA, USA.



The 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.


The 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.


At 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.


The 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.


allergic reaction; anaphylaxis; clinical notes; natural language processing; vaccine safety


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