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Updated: Aug 29, 2026

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
A prototype natural language interface to a large complex knowledge base, the Foundational Model of Anatomy
Gregory Distelhorst1, Vishrut Srivastava, Cornelius Rosse
1Departments of Biological Structure and Medical Education and Biomedical Informatics, University of Washington, Seattle, WA 98195, USA.
Abstract:
We describe a constrained natural language interface to a large knowledge base, the Foundational Model of Anatomy (FMA). The interface, called GAPP, handles simple or nested questions that can be parsed to the form, subject-relation-object, where subject or object is unknown. With the aid of domain-specific dictionaries the parsed sentence is converted to queries in the StruQL graph-searching query language, then sent to a server we developed, called OQAFMA, that queries the FMA and returns output as XML. Preliminary evaluation shows that GAPP has the potential to be used in the evaluation of the FMA by domain experts in anatomy.
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