Abstract
BackgroundWidespread 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.ObjectiveIn this paper, we present 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).MethodsCREATE 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.ResultsOur 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.ConclusionsThe 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.
Highlights
The widespread adoption of electronic health records has enabled the use of clinical data for clinical research and health care delivery [1]
A significant portion of relevant patient information is embedded as unstructured text, and natural language processing techniques such as information extraction are critical when using these data for clinical research [8,9,10,11]
We describe a proof-of-concept implementation of a cohort retrieval system—Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records (CREATE)—in which the same query to search both structured and unstructured text are used
Summary
The widespread adoption of electronic health records has enabled the use of clinical data for clinical research and health care delivery [1]. A significant portion of relevant patient information is embedded as unstructured text, and natural language processing techniques such as information extraction are critical when using these data for clinical research [8,9,10,11]. Methods: 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. Results: 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. Conclusions: 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
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