Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality

TL;DR

This paper introduces OMOP2OBO, an algorithm that maps EHR vocabularies to biomedical ontologies, enabling more comprehensive deep phenotyping and improving the identification of undiagnosed patients across hospitals.

Contribution

The paper presents a novel algorithm for automating the mapping of OMOP vocabularies to OBO ontologies, facilitating semantic integration of health data.

Findings

Mapped over 92,000 conditions and 8,600 drug ingredients to OBO ontologies.

Achieved 68-99% coverage of clinical concepts across 24 hospitals.

Enabled systematic identification of undiagnosed patients for genetic testing.

Abstract

Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. Objective: We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Results: Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. Conclusions: By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.