An exploratory study combining Virtual Reality and Semantic Web for life science research using Graph2VR

TL;DR

This paper explores how virtual reality can help scientists explore complex life science data using a tool called Graph2VR.

Contribution

The paper introduces three realistic life science use cases demonstrating the potential of Graph2VR for data exploration and enrichment.

Findings

Graph2VR can visualize metadata from large-scale cohort studies via the EUCAN Connect catalogue.

Genomic data from synthetic rare disease patients can be visualized using Graph2VR after processing with a variant interpretation pipeline.

Graph2VR can enrich graphs with external ontologies like the Dutch ATC code Ontology linked to Drugbank IDs.

Abstract

We previously described Graph2VR, a prototype that enables researchers to use virtual reality (VR) to explore and navigate through Linked Data graphs using SPARQL queries (see https://doi.org/10.1093/database/baae008). Here we evaluate the use of Graph2VR in three realistic life science use cases. The first use case visualizes metadata from large-scale multi-center cohort studies across Europe and Canada via the EUCAN Connect catalogue. The second use case involves a set of genomic data from synthetic rare disease patients, which was processed through the Variant Interpretation Pipeline and then converted into Resource Description Format for visualization. The third use case involves enriching a graph with additional information, in this case, the Dutch Anatomical Therapeutic Chemical code Ontology with the DrugID from Drugbank. These examples collectively showcase Graph2VR’s potential for data exploration and enrichment, as well as some of its limitations. We conclude that the endless three-dimensional space provided by VR indeed shows much potential for the navigation of very large knowledge graphs, and we provide recommendations for data preparation and VR tooling moving forward.

Database URL: https://doi.org/10.1093/database/baaf008

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