Work

Leveraging LLMs for Collaborative Ontology Engineering in Parkinson Disease Monitoring and Alerting

Year: 2026

Type: article

Abstract: Ontology engineering plays a critical role in clinical decision support systems for Parkinson’s Disease (PD) monitoring and alerting. While Large Language Models (LLMs) have shown promise in knowledge modeling tasks, their effectiveness in autonomously constructing comprehensive ontologies for complex clinical domains remains unclear. This study investigates four ontology engineering methodologies for PD monitoring and alerting: One-shot (OS) prompting, Decomposed Sequential Prompting (DSP), X-HCOME, and SimX-HCOME+. Multiple LLMs were evaluated across these methodologies. Generated ontologies were assessed against a reference PD ontology using structural evaluation metrics focused on classes and object properties. Expert review was additionally conducted to analyze knowledge extensions beyond the gold standard. LLMs were able to autonomously generate syntactically valid and semantically meaningful ontologies using OS and DSP prompting; however, these ontologies exhibited limited conceptual coverage. Incorporating human expertise through X-HCOME significantly improved ontology completeness and evaluation metrics. Expert review further validated clinically relevant concepts absent from the reference ontology. SimX-HCOME+ demonstrated that iterative, supervised collaboration supports ontology refinement, although challenges persisted in natural language-to-rule formalization. The findings suggest that LLMs are more effective as collaborative assistants rather than standalone ontology engineers in the PD domain. Structured human–LLM collaboration is associated with improved ontology coverage and facilitates the identification of potential knowledge extensions in clinical monitoring applications. While the present evaluation focuses primarily on structural ontology elements, the proposed methodologies provide useful insights for LLM-assisted ontology engineering in complex healthcare domains.

Source: AI

DOI: 10.3390/ai7040139

Authors: Georgios Bouchouras, Dimitrios Doumanas, Andreas Soularidis, Konstantinos Kotis, George Vouros

Institutions: University of the Aegean, University of Piraeus

Language: English

Topic: Biomedical Text Mining and Ontologies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,930