Towards cross-application model-agnostic federated cohort discovery

Abstract

Objectives: To demonstrate that 2 popular cohort discovery tools, Leaf and the Shared Health Research Information Network (SHRINE), are readily interoperable. Specifically, we adapted Leaf to interoperate and function as a node in a federated data network that uses SHRINE and dynamically generate queries for heterogeneous data models.

Materials and methods: SHRINE queries are designed to run on the Informatics for Integrating Biology & the Bedside (i2b2) data model. We created functionality in Leaf to interoperate with a SHRINE data network and dynamically translate SHRINE queries to other data models. We randomly selected 500 past queries from the SHRINE-based national Evolve to Next-Gen Accrual to Clinical Trials (ENACT) network for evaluation, and an additional 100 queries to refine and debug Leaf's translation functionality. We created a script for Leaf to convert the terms in the SHRINE queries into equivalent structured query language (SQL) concepts, which were then executed on 2 other data models.

Results and discussion: 91.1% of the generated queries for non-i2b2 models returned counts within 5% (or ±5 patients for counts under 100) of i2b2, with 91.3% recall. Of the 8.9% of queries that exceeded the 5% margin, 77 of 89 (86.5%) were due to errors introduced by the Python script or the extract-transform-load process, which are easily fixed in a production deployment. The remaining errors were due to Leaf's translation function, which was later fixed.

Conclusion: Our results support that cohort discovery applications such as Leaf and SHRINE can interoperate in federated data networks with heterogeneous data models.

Keywords: clinical trials; cohort discovery; electronic health records; interoperability.