Linking Dispense Data to Electronic Health Orders: Tutorial for Querying Commercial Pharmacy Databases to Support Systemwide Quality Improvement

Abstract Background Assessing medication adherence is central to quality care, yet linking electronic health record (EHR) medication orders to outpatient pharmacy dispense data remains technically complex. Objective This study aimed to present a generalized, reproducible tutorial for linking EHR medication orders to pharmacy dispense data that can be used to assess medication dispense proportions. Methods We developed and validated a structured query approach to link EHR medication orders to external pharmacy dispense data using patient identifiers, medication-level identifiers, pharmacy identifiers, and temporal constraints. The tutorial emphasizes key design decisions, including handling multiple triggering events, deduplication across vendors, and managing formulation changes. A retrospective cohort of pediatric acute otitis media encounters (January 1, 2021, to January 1, 2024) was used as an illustrative example. Results Overall, 98.3% (302/307) of pharmacies in the cohort returned at least 1 dispense record during the study period and were therefore classified as reporting pharmacies. Among 3404 orders, 2616 (76.9%) had a recorded dispense. Conclusions EHR-integrated pharmacy data provide a feasible, timely proxy for assessing medication adherence. This tutorial provides a scalable framework for linking EHR and pharmacy data for medication adherence studies, while highlighting key methodological considerations for SQL coding.