On Cohort Retrieval System from Clinical Data Repositories using OMOP Common Data Model: A Proof-of-Concept Implementation (Preprint)

Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William Hersh, Hongfang Liu
2019 JMIR Medical Informatics  
Widespread adoption of electronic health records has enabled the secondary use of electronic health record data for clinical research and health care delivery. Natural language processing techniques have shown promise in their capability to extract the information embedded in unstructured clinical data, and information retrieval techniques provide flexible and scalable solutions that can augment natural language processing systems for retrieving and ranking relevant records. In this paper, we
more » ... esent the implementation of a cohort retrieval system that can execute textual cohort selection queries on both structured data and unstructured text-Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records (CREATE). CREATE is a proof-of-concept system that leverages a combination of structured queries and information retrieval techniques on natural language processing results to improve cohort retrieval performance using the Observational Medical Outcomes Partnership Common Data Model to enhance model portability. The natural language processing component was used to extract common data model concepts from textual queries. We designed a hierarchical index to support the common data model concept search utilizing information retrieval techniques and frameworks. Our case study on 5 cohort identification queries, evaluated using the precision at 5 information retrieval metric at both the patient-level and document-level, demonstrates that CREATE achieves a mean precision at 5 of 0.90, which outperforms systems using only structured data or only unstructured text with mean precision at 5 values of 0.54 and 0.74, respectively. The implementation and evaluation of Mayo Clinic Biobank data demonstrated that CREATE outperforms cohort retrieval systems that only use one of either structured data or unstructured text in complex textual cohort queries.
doi:10.2196/17376 pmid:33021486 fatcat:jnr452ywrzbuhajeamukcb4aqi