Related Experiment Video
Updated: Feb 17, 2026
Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
SATORI: a system for ontology-guided visual exploration of biomedical data repositories
Fritz Lekschas1,2, Nils Gehlenborg2
1Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA 02138, USA.
Motivation:
The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest.
Results:
We developed SATORI-an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection. SATORI enables researchers to seamlessly search, browse and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface.
Availability And Implementation:
SATORI is an open-source web application, which is freely available at http://satori.refinery-platform.org and integrated into the Refinery Platform.
Contact:
nils@hms.harvard.edu.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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