The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality

Andreas Bueckle; Catherine Qing; Catherine Qing; Shefali Luley; Yash Kumar; Naval Pandey; Katy Börner

doi:10.3389/fbinf.2023.1162723

Frontiers in Bioinformatics (Apr 2023)

The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality

Andreas Bueckle,
Catherine Qing,
Catherine Qing,
Shefali Luley,
Yash Kumar,
Naval Pandey,
Katy Börner

Affiliations

Andreas Bueckle: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States
Catherine Qing: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States
Catherine Qing: Department of Humanities and Sciences, Stanford University, Stanford, CA, United States
Shefali Luley: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States
Yash Kumar: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States
Naval Pandey: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States
Katy Börner: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, United States

DOI: https://doi.org/10.3389/fbinf.2023.1162723
Journal volume & issue: Vol. 3

Abstract

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The Human Reference Atlas (HRA, https://humanatlas.io) funded by the NIH Human Biomolecular Atlas Program (HuBMAP, https://commonfund.nih.gov/hubmap) and other projects engages 17 international consortia to create a spatial reference of the healthy adult human body at single-cell resolution. The specimen, biological structure, and spatial data that define the HRA are disparate in nature and benefit from a visually explicit method of data integration. Virtual reality (VR) offers unique means to enable users to explore complex data structures in a three-dimensional (3D) immersive environment. On a 2D desktop application, the 3D spatiality and real-world size of the 3D reference organs of the atlas is hard to understand. If viewed in VR, the spatiality of the organs and tissue blocks mapped to the HRA can be explored in their true size and in a way that goes beyond traditional 2D user interfaces. Added 2D and 3D visualizations can then provide data-rich context. In this paper, we present the HRA Organ Gallery, a VR application to explore the atlas in an integrated VR environment. Presently, the HRA Organ Gallery features 55 3D reference organs, 1,203 mapped tissue blocks from 292 demographically diverse donors and 15 providers that link to 6,000+ datasets; it also features prototype visualizations of cell type distributions and 3D protein structures. We outline our plans to support two biological use cases: on-ramping novice and expert users to HuBMAP data available via the Data Portal (https://portal.hubmapconsortium.org), and quality assurance/quality control (QA/QC) for HRA data providers. Code and onboarding materials are available at https://github.com/cns-iu/hra-organ-gallery-in-vr.

Published in Frontiers in Bioinformatics

ISSN: 2673-7647 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Medicine: Medicine (General): Computer applications to medicine. Medical informatics
Website: https://www.frontiersin.org/journals/bioinformatics

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