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A cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data


Bao SShunxing , Chiron SSophie , Tang YYucheng , Heiser CNCody N , Southard-Smith ANAustin N , Lee HHHo Hin , Ramirez MAMarisol A , Huo YYuankai , Washington MKMary K , Scoville EAElizabeth A , Roland JTJoseph T , Liu QQi , Lau KSKen S , Wilson KTKeith T , Coburn LALori A , Landman BABennett A . Proceedings of SPIE--the International Society for Optical Engineering. 2021 2 15; 11601().


The Gut Cell Atlas (GCA), an initiative funded by the Helmsley Charitable Trust, seeks to create a reference platform to understand the human gut, with a specific focus on Crohn’s disease. Although a primary focus of the GCA is on focusing on single-cell profiling, we seek to provide a framework to integrate other analyses on multi-modality data such as electronic health record data, radiological images, and histology tissues/images. Herein, we use the research electronic data capture (REDCap) system as the central tool for a secure web application that supports protected health information (PHI) restricted access. Our innovations focus on addressing the challenges with tracking all specimens and biopsies, validating manual data entry at scale, and sharing organizational data across the group. We present a scalable, cross-platform barcode printing/record system that integrates with REDCap. The central informatics infrastructure to support our design is a tuple table to track longitudinal data entry and sample tracking. The current data collection (by December 2020) is illustrated with types and formats of the data that the system collects. We estimate that one terabyte is needed for data storage per patient study. Our proposed data sharing informatics system addresses the challenges with integrating physical sample tracking, large files, and manual data entry with REDCap.