NIAID

HGRepo Informatics Framework for the NIAID/DIR COVID-19 Immune Response Consortium

Sandhya Xirasagar Ph.D., Lead, Clinical and Laboratory Informatics Section with NIAID

Jason Barnett, Contract Lead, Medical Science and Computing, Inc

NIAID partnered with LabKey to develop an informatics system to host clinical data collected internationally for the Immune Response to COVID-19 research project. This presentation covers the informatics framework including the background and requirements for the scientific data management system, a demo of HGRepo and the future vision for the system.

The presentation delves into the creation and implementation of the HE Repo Informatics Framework by the NIAID Division of Intramural Research for the COVID-19 Immune Response Consortium. This framework was specially designed to manage the intricacies of data collection and analysis across multiple international and domestic hospital sites, focusing on natural history studies of COVID-19 rather than clinical trials. The initiative faced the challenge of handling unstructured data from a variety of sources, including both electronic and paper records, which necessitated a flexible and robust data management solution.

To address these challenges, the consortium employed LabKey, a platform known for its capacity to structure, standardize, and prepare data for analysis. LabKey’s selection was pivotal for its ability to accommodate multiple data capture modes, ensuring sustainability and adaptability to the diverse data formats encountered, ranging from structured Excel files to screenshots of paper records. This choice allowed for the effective linkage of patient samples with assay data, facilitating collaborative research efforts.

The implementation of LabKey was marked by a rapid deployment timeline, with the platform going live within a matter of weeks from its introduction to the consortium. This swift setup enabled the immediate commencement of data collection and analysis, which was crucial given the urgency imposed by the pandemic. The platform’s flexibility was further demonstrated through its support for role-based collaborative access, integration with external data sources for assay data, and the provision of tools for standardization, querying, sharing, and visualization of data.

Moreover, the framework capitalized on the collaborative spirit engendered by the COVID-19 research urgency, bringing together a diverse group of stakeholders including data curators, medical experts, data scientists, and system developers. This multidisciplinary approach facilitated the establishment of a comprehensive system that not only addressed the immediate data management needs but also laid the groundwork for future enhancements, such as the integration of additional data sets and the use of ontologies for more sophisticated data handling.

In summary, the HE Repo Informatics Framework represents a significant achievement in the management of complex, unstructured data for pandemic research. Through the effective use of LabKey and the collaborative effort of a wide range of contributors, the consortium was able to quickly establish a system that supported the dynamic and urgent needs of COVID-19 research, enabling the collection, analysis, and sharing of critical data to advance the understanding and treatment of the disease.

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