A Comprehensive Portal for Clinical and Translational Data Warehouses

Abstract

Data-driven methods in biomedical research can help to obtain new insights into the development, progression and therapy of diseases. Clinical and translational data warehouses such as Informatics for Integrating Biology and the Bedside (i2b2) and tranSMART are important solutions for this. From the well-known FAIR data principles, which are used to address the aspects of findability, accessibility, interoperability and reusability. In this paper, we focus on findability. For this purpose, we describe a portal solution that acts as a catalogue for a wide range of data warehouse instances, featuring a central access point and links to training material, such as user manuals and video tutorials. Moreover, the portal provides an overview of the status of multiple warehouses for developers and a set of statistics about the data currently loaded. Due to its modular design and the use of modern web technologies, the portal is easy to extend and customize to reflect different corporate designs and institutional requirements.

Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review

“…The core of data flow in the data management system is the Translational Data Warehouse (TDW) [ 24 ] based on Informatics for Integrating Biology & the Bedside (I2B2) core technology. [ 25 ] TDW aggregates data from pre‐clinical and clinical data sources.…”

“…[ 26 ] Clinical and research data sources include clinical electronic medical records such as Epic, [ 27 ] and Public Health Sciences’ research databases, clinical research imaging, clinical registries, and data from various clinic centers. [ 24 ] The I2B2 framework [ 25 ] is a platform designed to support the integration and analysis of heterogeneous biomedical data, and it uses ETL processes to extract data from various sources, transform it into a standard format, and load it into the data warehouse. ETL processes are used to integrate data from different sources, such as electronic health records, imaging systems, genomic databases, and so on.…”