Steven Bedrick

A Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data

Steve R Chamberlin, Steven D. Bedrick, Aaron M. Cohen, Yanshan Wang, Andrew Wen, Sijia Liu, Hongfang Liu, William Hersh
medRxiv, Jan 2019


Performance of systems used for patient cohort identification with electronic health record (EHR) data is not well-characterized. The objective of this research was to evaluate factors that might affect information retrieval (IR) methods and to investigate the interplay between commonly used IR approaches and the characteristics of the cohort definition structure. We used an IR test collection containing 56 test patient cohort definitions, 100,000 patient records originating from an academic medical institution EHR data warehouse, and automated word-base query tasks, varying four parameters. Performance was measured using B-Pref. We then designed 59 taxonomy characteristics to classify the structure of the 56 topics. In addition, six topic complexity measures were derived from these characteristics for further evaluation using a beta regression simulation. We did not find a strong association between the 59 taxonomy characteristics and patient retrieval performance, but we did find strong performance associations with the six topic complexity measures created from these characteristics, and interactions between these measures and the automated query parameter settings. Some of the characteristics derived from a query taxonomy could lead to improved selection of approaches based on the structure of the topic of interest. Insights gained here will help guide future work to develop new methods for patient-level cohort discovery with EHR data.Competing Interest StatementSteven Chamberlin, Aaron Cohen, and William Hersh have research funding from AlnylamPharmaceuticals that is unrelated to the work described in this paper.Funding StatementNational Institutes of Health National Library of Medicine Grant 1R01LM011934Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesOur data contains patient health information and cannot be made publicly available.

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