Facilitating phenotype transfer using a common data model

Abstract

Background: Implementing clinical phenotypes across a network is labor intensive and potentially error prone. Use of a common data model may facilitate the process.

Methods: Electronic Medical Records and Genomics (eMERGE) sites implemented the Observational Health Data Sciences and Informatics (OHDSI) Observational Medical Outcomes Partnership (OMOP) Common Data Model across their electronic health record (EHR)-linked DNA biobanks. Two previously implemented eMERGE phenotypes were converted to OMOP and implemented across the network.

Results: It was feasible to implement the common data model across sites, with laboratory data producing the greatest challenge due to local encoding. Sites were then able to execute the OMOP phenotype in less than one day, as opposed to weeks of effort to manually implement an eMERGE phenotype in their bespoke research EHR databases. Of the sites that could compare the current OMOP phenotype implementation with the original eMERGE phenotype implementation, specific agreement ranged from 100% to 43%, with disagreements due to the original phenotype, the OMOP phenotype, changes in data, and issues in the databases. Using the OMOP query as a standard comparison revealed differences in the original implementations despite starting from the same definitions, code lists, flowcharts, and pseudocode.

Conclusion: Using a common data model can dramatically speed phenotype implementation at the cost of having to populate that data model, though this will produce a net benefit as the number of phenotype implementations increases. Inconsistencies among the implementations of the original queries point to a potential benefit of using a common data model so that actual phenotype code and logic can be shared, mitigating human error in reinterpretation of a narrative phenotype definition.

Keywords: Common data model; Electronic health records; Phenotyping.

Conflict of interest statement

Conflicts of interest:

None reported.

Copyright © 2019 Elsevier Inc. All rights reserved.

Figures

Figure 1.. Phenotyping flowchart and issues reported.

Phenotypes were based on the published eMERGE phenotype definition, which included a narrative definition, high-level concept code lists, a flowchart, and pseudocode, and it was taken as the gold standard definition and therefore had no issues. The original eMERGE implementation had each local site write software to query their local database based on the eMERGE definition. In this study, each site converted its data to the OHDSI OMOP database using extract-transfer-load (ETL) software and OMOP vocabulary mappings. The eMERGE definition was encoded as a single OMOP phenotype using the OHDSI Atlas tool. A site could use a local copy of Atlas running on their OMOP database to run the phenotype or use SQL that was generated automatically by Atlas for five database management systems. Where possible, the OMOP result of the phenotype query was compared to the original result. Sites reported issues that they encountered, which are shown in grey squares adjacent to the most relevant step. Issues that caused a significant difference between the original and OMOP query are marked with a star in bold. Those that caused a moderate difference are marked with a star in non-bold. Issues that caused little or no change are marked with a smaller round bullet in a smaller font.