Conversion of Sensitive Data to the Observational Medical Outcomes Partnership Common Data Model: Protocol for the Development and Use of Carrot.

Abstract

Background: The use of data standards is low across the health care system, and converting data to a common data model (CDM) is usually required to undertake international research. One such model is the Observational Medical Outcomes Partnership (OMOP) CDM. It has gained substantial traction across researchers and those who have developed data platforms. The Observational Health Care Data Sciences and Informatics (OHDSI) partnership manages OMOP and provides many open-source tools to assist in converting data to the OMOP CDM. The challenge, however, is in the skills, knowledge, know-how, and capacity within teams to convert their data to OMOP. The European Health Care Data Evidence Network provided funds to allow data owners to bring in external resources to do the required conversions. The Carrot software (University of Nottingham) is a new set of open-source tools designed to help address these challenges while not requiring data access by external resources.

Objective: The use of data protection rules is increasing, and privacy by design is a core principle under the European and UK legislations related to data protection. Our aims for the Carrot software were to have a standardized mechanism for managing the data curation process, capturing the rules used to convert the data, and creating a platform that can reuse rules across projects to drive standardization of process and improve the speed without compromising on quality. Most importantly, we aimed to deliver this design-by-privacy approach without requiring data access to those creating the rules.

Methods: The software was developed using Agile approaches by both software engineers and data engineers, who would ultimately use the system. Experts in OMOP were used to ensure the approaches were correct. An incremental release program was initiated to ensure we delivered continuous progress.

Results: Carrot has been delivered and used on a project called COVID-Curated and Open Analysis and Research Platform (CO-CONNECT) to assist in the process of allowing datasets to be discovered via a federated platform. It has been used to create over 45,000 rules, and over 5 million patient records have been converted. This has been achieved while maintaining our principle of not allowing access to the underlying data by the team creating the rules. It has also facilitated the reuse of existing rules, with most rules being reused rather than manually curated.

Conclusions: Carrot has demonstrated how it can be used alongside existing OHDSI tools with a focus on the mapping stage. The COVID-Curated and Open Analysis and Research Platform project successfully managed to reuse rules across datasets. The approach is valid and brings the benefits expected, with future work continuing to optimize the generation of rules.

International registered report identifier (irrid): RR1-10.2196/60917.