The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink
- PMID: 31797475
- PMCID: PMC7528887
- DOI: 10.1002/pds.4919
The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink
Abstract
Purpose: 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.
Methods: 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.
Results: 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.
Conclusions: 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.
Keywords: allergic reaction; anaphylaxis; clinical notes; natural language processing; vaccine safety.
© 2019 John Wiley & Sons, Ltd.
Conflict of interest statement
CONFLICT OF INTEREST
The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
Similar articles
-
Identifying Cases of Shoulder Injury Related to Vaccine Administration (SIRVA) in the United States: Development and Validation of a Natural Language Processing Method.JMIR Public Health Surveill. 2022 May 24;8(5):e30426. doi: 10.2196/30426. JMIR Public Health Surveill. 2022. PMID: 35608886 Free PMC article.
-
Identifying Patients With Hypoglycemia Using Natural Language Processing: Systematic Literature Review.JMIR Diabetes. 2022 May 16;7(2):e34681. doi: 10.2196/34681. JMIR Diabetes. 2022. PMID: 35576579 Free PMC article. Review.
-
Natural Language Processing Combined with ICD-9-CM Codes as a Novel Method to Study the Epidemiology of Allergic Drug Reactions.J Allergy Clin Immunol Pract. 2020 Mar;8(3):1032-1038.e1. doi: 10.1016/j.jaip.2019.12.007. Epub 2019 Dec 16. J Allergy Clin Immunol Pract. 2020. PMID: 31857264 Free PMC article.
-
Capturing anaphylaxis through medical records: Are ICD and CPT codes sufficient?Ann Allergy Asthma Immunol. 2020 Feb;124(2):150-155. doi: 10.1016/j.anai.2019.11.026. Epub 2019 Nov 27. Ann Allergy Asthma Immunol. 2020. PMID: 31785369 Review.
-
The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink.Int J Med Inform. 2019 Jul;127:27-34. doi: 10.1016/j.ijmedinf.2019.04.009. Epub 2019 Apr 13. Int J Med Inform. 2019. PMID: 31128829 Free PMC article.
Cited by
-
Research data warehouse: using electronic health records to conduct population-based observational studies.JAMIA Open. 2023 Jun 21;6(2):ooad039. doi: 10.1093/jamiaopen/ooad039. eCollection 2023 Jul. JAMIA Open. 2023. PMID: 37359950 Free PMC article.
-
Measurement of provider fidelity to immunization guidelines: a mixed-methods study on the feasibility of documenting patient refusals of the human papillomavirus vaccine.BMC Med Inform Decis Mak. 2022 Dec 22;22(1):339. doi: 10.1186/s12911-022-02083-2. BMC Med Inform Decis Mak. 2022. PMID: 36550466 Free PMC article.
-
Improving Methods of Identifying Anaphylaxis for Medical Product Safety Surveillance Using Natural Language Processing and Machine Learning.Am J Epidemiol. 2023 Feb 1;192(2):283-295. doi: 10.1093/aje/kwac182. Am J Epidemiol. 2023. PMID: 36331289 Free PMC article.
-
Information systems for vaccine safety surveillance.Hum Vaccin Immunother. 2022 Nov 30;18(6):2100173. doi: 10.1080/21645515.2022.2100173. Epub 2022 Sep 26. Hum Vaccin Immunother. 2022. PMID: 36162040 Free PMC article. Review.
-
Identification of Preterm Labor Evaluation Visits and Extraction of Cervical Length Measures from Electronic Health Records Within a Large Integrated Health Care System: Algorithm Development and Validation.JMIR Med Inform. 2022 Sep 6;10(9):e37896. doi: 10.2196/37896. JMIR Med Inform. 2022. PMID: 36066930 Free PMC article.
References
-
- Sampson HA, Muñoz-Furlong A, Campbell RL, et al. Second symposium on the definition and management of anaphylaxis: Summary report—Second National Institute of Allergy and Infectious Disease/ Food Allergy and Anaphylaxis Network symposium. J Allergy Clin Immunol. 2006;117(2):391–397. - PubMed
-
- Tintinalli JE, Stapczynski JS, Ma OJ, Yealy DM, Meckler GD, Cline DM. Tintinalli’s emergency medicine: a comprehensive study guide. New York, NY: McGraw-Hill; 2016.
-
- Archived web page collected at the request of National Institute of Allergy and Infectious Diseases using Archive-It. This page was captured on Sep 06, 2016 and is part of the Public Website Archive. Archive collection 2016. https://wayback.archive-it.org/7761/20160906160831/http://www.niaid.nih.gov/topics/anaphylaxis/pages/default.aspx?wt.ac=bcN.... Accessed February 4, 2016.
-
- Madaan A, Maddox DE. Vaccine allergy: diagnosis and management. Immunol Allergy Clin. 2003;23(4):555–588. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Medical