TY  - JOUR
AU  - Seinen, Tom M
AU  - Kors, Jan A
AU  - van Mulligen, Erik M
AU  - Rijnbeek, Peter R
PY  - 2025
DA  - 2025/2/13
TI  - Using Structured Codes and Free-Text Notes to Measure Information Complementarity in Electronic Health Records: Feasibility and Validation Study
JO  - J Med Internet Res
SP  - e66910
VL  - 27
KW  - natural language processing
KW  - named entity recognition
KW  - clinical concept extraction
KW  - machine learning
KW  - electronic health records
KW  - EHR
KW  - word embeddings
KW  - clinical concept similarity
KW  - text mining
KW  - code
KW  - free-text
KW  - information
KW  - electronic record
KW  - data
KW  - patient records
KW  - framework
KW  - structured data
KW  - unstructured data
AB  - Background: Electronic health records (EHRs) consist of both structured data (eg, diagnostic codes) and unstructured data (eg, clinical notes). It is commonly believed that unstructured clinical narratives provide more comprehensive information. However, this assumption lacks large-scale validation and direct validation methods. Objective: This study aims to quantitatively compare the information in structured and unstructured EHR data and directly validate whether unstructured data offers more extensive information across a patient population. Methods: We analyzed both structured and unstructured data from patient records and visits in a large Dutch primary care EHR database between January 2021 and January 2024. Clinical concepts were identified from free-text notes using an extraction framework tailored for Dutch and compared with concepts from structured data. Concept embeddings were generated to measure semantic similarity between structured and extracted concepts through cosine similarity. A similarity threshold was systematically determined via annotated matches and minimized weighted Gini impurity. We then quantified the concept overlap between structured and unstructured data across various concept domains and patient populations. Results: In a population of 1.8 million patients, only 13% of extracted concepts from patient records and 7% from individual visits had similar structured counterparts. Conversely, 42% of structured concepts in records and 25% in visits had similar matches in unstructured data. Condition concepts had the highest overlap, followed by measurements and drug concepts. Subpopulation visits, such as those with chronic conditions or psychological disorders, showed different proportions of data overlap, indicating varied reliance on structured versus unstructured data across clinical contexts. Conclusions: Our study demonstrates the feasibility of quantifying the information difference between structured and unstructured data, showing that the unstructured data provides important additional information in the studied database and populations. The annotated concept matches are made publicly available for the clinical natural language processing community. Despite some limitations, our proposed methodology proves versatile, and its application can lead to more robust and insightful observational clinical research. 
SN  - 1438-8871
UR  - https://www.jmir.org/2025/1/e66910
UR  - https://doi.org/10.2196/66910
DO  - 10.2196/66910
ID  - info:doi/10.2196/66910
ER  -