Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas

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To enable the Human BioMolecular Atlas Program (HuBMAP) Consortium production phase, we will develop several new and improved spatial single cell and bioimaging data visualization features. These include Vitessce support for large volume 3D data combined with 2D maps, spatial queries in 2D maps via HuBMAP Data Portal UI and Vitessce, user workspaces with support for co-analysis of community and HuBMAP data, “datahubs” for external data that can be displayed in context of Human Reference Atlas and HuBMAP data, new file formats for 3D spatial data, deployment of generalized “cell x gene” matrix format across HuBMAP Data Portal, ability to store and share analyses of data conducted with analysis workspaces, integration of Vitessce with Common Coordinate Framework navigation tools, UI enhancements to scale to growing body of HuBMAP data (both in terms of volume and richness of the data and analysis results), seamless integration between evolving Human Reference Atlas UI and Data Portal UI. Furthermore, we will research solutions for (1) Seamless navigation through HuBMAP and integrated community data through visual interfaces that combine data portal UI, human reference atlas UI, and interactive visualization tools, e.g., Vitessce. (2) Extension of Vitessce to support interpretation of functional single-cell and tissue data through network and pathway visualizations that support 2D and 3D spatial information. (3) Rollout of “data hubs”, i.e., formats and annotation standards for spatial single-cell and tissue data that can be viewed in the context of the Human Reference Atlas (similar to “track hubs” for genome browsers). (4) UI-based analysis workspaces to assemble execution pipelines for data processing and visualization.