3D Human Reference Body: Multiscale Exploration and Visualization of Biomolecular Data in Virtual Reality

Project Summary/Abstract (30 lines of text) We propose the research and development of a novel, 3D, immersive, virtual reality (VR) exploration tool using a federated collection of datasets from three Common Fund Data Ecosystem (CFDE) efforts: Human BioMolecular Atlas Program1,2 (HuBMAP), Cellular Senescence Network3 (SenNet), and Genotype-Tissue Expression4 (GTEx). The Aim of this proposal is to Enable FAIR5 access to datasets from these three Common Fund programs via an immersive VR interface with embedded 2D/3D visualizations. Using existing, Linked Open Data (LOD) infrastructure built for the Human Reference Atlas (HRA)6–9, we will Federate cell summaries from datasets and extraction sites across three Common Fund programs in the HRA6–9 (Sub-Aim 1), i.e., we will identify datasets that have been registered into HRA 3D Reference Objects (organs) via dedicated tools8, thus giving them a 3D extraction site; then, we will retrieve existing cell summaries for these extraction sites and registered datasets given existing cell-by-gene matrices or proteomics markers (462 datasets as of June 14, 2024). For the related Sub-Aim 2, we will Deploy CFDE datasets in the HRA Organ Gallery in VR, an existing research prototype for a VR application that allows the immersive exploration of this multiscale, multimodal data. Building on our prior research on Data Visualization Literacy, VR, and immersive analytics10–12, we will add 2D and 3D visualization capabilities to the HRA Organ Gallery to visualize cell summaries at the dataset, 3D extraction site, and anatomical structure (atlas) level. All cell summaries will be connected to 3D registration sites inside one of 65 existing 3D reference organs (spatial), annotated with anatomical structure(s) that are aligned to the UBERON13 ontology (biological structure), and associated with clinical (donor) metadata, such as age, sex, race, etc. All work and code will be documented and made available to the community. Additionally, we will update existing and create new training and instructions materials, not only in written form, but also as videos and inside the HRA Organ Gallery in VR application. Further, we are planning extensive demonstrations of this work at CFDE meetings and at various events organized for HuBMAP, SenNet, and GTEx researchers.