Ontology Refinement with Embeddings and LLMs: A Case Study on CASTON

Ontologies are useful structures to organize and maintain information that can be understood both by humans and systems. However, since their manual crafting is a laborious task, many specific domains lack reference ontologies. The outstanding ability for understanding natural language demonstrated by the Large Language Models (LLMs) has motivated their application to aid on a variety of fields, including on ontology development. This work presents the experimentation with a technique that uses LLMs in the role of domain experts to build conceptual hierarchies for a given initial concept. Twenty ontologies automatically constructed for the domain of the Brazilian maritime territory (a.k.a the Blue Amazon) using GPT-3.5 and GPT-4 were then evaluated by human experts. The models were able to construct overall coherent conceptualizations of the domain, but none of the outputs was completely satisfactory as a representation of the context without refinement.

Ontology learning (OL) aims to automatically construct structured knowledge models from text, yet progress remains fragmented across methods, domains, and evaluation practices. Despite decades of research, OL lacks a shared infrastructure for systematic evaluation and ontology access. This absence has hindered progress and fragmented research, leaving the central challenges of OL largely unaddressed. We introduce OntoLearner, a modular, cross-domain, and first-of-its-kind framework that unifies ontology access, large language model (LLM)-driven learning pipelines, and standardized benchmarking. OntoLearner releases 180 machine-readable ontologies spanning 22 domains and provides pipeline-ready datasets with train/dev/test splits for three core OL tasks: term typing, taxonomy discovery, and non-taxonomic relation extraction. Using this infrastructure, we conduct a large-scale empirical study of OL, evaluating 22 retrieval models and 12 LLMs across domains and tasks. The results converge on a finding that reframes the central challenge of OL: failure modes scale with ontological complexity rather than model size or architectural sophistication. The primary bottleneck is not model capability, but a structural mismatch between how models encode knowledge and how ontologies organize it. These findings establish that effective OL is reachable through the cross-domain, multi-task benchmarking enabled by OntoLearner. OntoLearner is open-source (MIT license) at https://github.com/sciknoworg/OntoLearner/.

Knowledge Organization Systems like Ontologies and taxonomies are fundamental for structuring scientific knowledge, yet their manual curation presents a persistent bottleneck in knowledge management. While Large Language Models (LLMs) offer a scalable mechanism for automated ontology generation, their capacity to classify complex, domain-specific semantics requires systematic evaluation. In this paper, we assess the performance of five small, open-source LLMs (up to 9 billion parameters) in identifying semantic relationships between biomedical concepts. To support this evaluation, we introduce MeSH-Rel-4K, a dataset comprising 4K semantic relationships extracted from the Medical Subject Headings (MeSH). We analyse three adaptation strategies: standard prompting, Chain-of-Thought prompting, and fine-tuning. While parameter-constrained models traditionally struggle with the nuances of in-context logic, our results reveal that targeted fine-tuning increases the average F1-score by 34.1 percentage points. These results confirm that direct fine-tuning effectively exceeds the reasoning bottlenecks of smaller LLMs, providing an accurate, automated methodology for the construction and evolution of specialised biomedical ontologies.