Development of an Open-Source Annotated Glaucoma Medication Dataset From Clinical Notes in the Electronic Health Record

Abstract

Purpose To describe the methods involved in processing and characteristics of an open dataset of annotated clinical notes from the electronic health record (EHR) annotated for glaucoma medications. Methods In this study, 480 clinical notes from office visits, medical record numbers (MRNs), visit identification numbers, provider names, and billing codes were extracted for 480 patients seen for glaucoma by a comprehensive or glaucoma ophthalmologist from January 1, 2019, to August 31, 2020. MRNs and all visit data were de-identified using a hash function with salt from the deidentifyr package. All progress notes were annotated for glaucoma medication name, route, frequency, dosage, and drug use using an open-source annotation tool, Doccano. Annotations were saved separately. All protected health information (PHI) in progress notes and annotated files were de-identified using the published de-identifying algorithm Philter. All progress notes and annotations were manually validated by two ophthalmologists to ensure complete de-identification. Results The final dataset contained 5520 annotated sentences, including those with and without medications, for 480 clinical notes. Manual validation revealed 10 instances of remaining PHI which were manually corrected. Conclusions Annotated free-text clinical notes can be de-identified for upload as an open dataset. As data availability increases with the adoption of EHRs, free-text open datasets will become increasingly valuable for “big data” research and artificial intelligence development. This dataset is published online and publicly available at https://github.com/jche253/Glaucoma_Med_Dataset . Translational Relevance This open access medication dataset may be a source of raw data for future research involving big data and artificial intelligence research using free-text.

GRAPE: A multi-modal dataset of longitudinal follow-up visual field and fundus images for glaucoma management

“…The progression analysis was performed on part of VFs. Annotated Glaucoma Medication Dataset 26 : This is an open-source dataset including 480 clinical notes from the Electronic Health Record (EHR) system. All progress notes were annotated for glaucoma medication name, route, frequency, dosage, and drug use.…”