Building an i2b2-Based Population Repository for COVID-19 Research

Abstract

Reuse of Electronic Health Records (EHRs) for specific diseases such as COVID-19 requires data to be recorded and persisted according to international standards. Since the beginning of the COVID-19 pandemic, Hospital Universitario 12 de Octubre (H12O) evolved its EHRs: it identified, modeled and standardized the concepts related to this new disease in an agile, flexible and staged way. Thus, data from more than 200,000 COVID-19 cases were extracted, transformed, and loaded into an i2b2 repository. This effort allowed H12O to share data with worldwide networks such as the TriNetX platform and the 4CE Consortium.

TransformEHRs: a flexible methodology for building transparent ETL processes for EHR reuse

“…For this purpose, the DCM-based methodology previously proposed by Pedrera-Jiménez et al, for obtaining EHR-derived datasets for research 5 was used, which is composed of four phases: (1) health condition analysis and specification of important variables, (2) modeling and formalization of the concepts of the clinical domain, (3) definition of rules to generate EHR-derived models, and (4) implementation and validation of the methodology. This study allowed H12O to participate, during the COVID-19 pandemic, in different international health data initiatives such as the ISARIC Consortium, the EHDEN Consortium, the 4CE Consortium, and the TriNetX Platform, 9 10 11 12 without requiring manual recording effort parallel to COVID-19 patient health care. 20 However, it is necessary to continue its development to improve each of its component phases.…”

“…Thus, to define the set of operations, different data models used in several data-driven projects in H12O were analyzed, 9 10 11 12 considering the typologies described above. Table 3 shows the list of specifications reviewed, the type of data model they incorporate, and their purpose.…”

“…COVID-19 use case has been selected to apply the methodology proposed, in order to improve the transparency of EHR reuse processes for the many data initiatives that have emerged around this new and unknown health condition at H12O. [9][10][11][12] The methodology was valuable and innovative in this pandemic scenario, where data were urgently needed to study this disease and neither the time nor the resources were available to conduct manual data recording or to thoroughly evaluate data collection processes. Despite this, the methodology is, by design, applicable to other health conditions and flexible to be adopted by any organization, through parameterization mechanisms according to the restrictions of data sources and data outputs.…”

“…There are specifications that have become standards for this type of resources, such as the i2b2 model, 35 implemented in tools such as TriNetX, 11 and OMOP CDM, 36 adopted in international consortia such as EHDEN. Thus, to define the set of operations, different data models used in several data-driven projects in H12O were analyzed, [9][10][11][12] considering the typologies described above. ►Table 3 shows the list of specifications reviewed, the type of data model they incorporate, and their purpose.…”

“…7 In the context of coronavirus disease 2019 (COVID- 19), this line of work has allowed H12O to participate in an efficient and sustainable way, during the most critical moments of the pandemic, in several real world data (RWD) initiatives, 8 such as the 4CE Consortium, 9 the EHDEN Consortium, 10 and Tri-NetX. 11 Similarly, it has made it possible to optimize data collection in frequently manual processes, such as the automated data loading into the case report form (CRF) of the ISARIC-WHO Consortium. 12 However, these EHR reuse processes are often based on black boxes on which the final data customer is unaware of how the data uploaded to their research database were recorded, extracted, and transformed.…”