arXiv:2611.12095v1 Announce Type: new
Abstract: Biomedical ontologies are structured knowledge systems that must evolve continuously to represent newly emerging knowledge, but their manual maintenance remains time-consuming and laborintensive. Textual definitions are especially costly because they must be readable to humans and compatible with controlled entities, relations, and logical constraints. Large language models (LLMs) offer a promising way to assist ontology engineering tasks, including definition generation. However, textual plausibility does not guarantee knowledge-system compatibility. A generated definition may be fluent and close to a reference definition, yet still fail to ground its implied entities or violate ontology-level constraints. Directly inserting such definitions into ontology libraries may therefore introduce entity-level hallucinations and logical inconsistencies. To address this problem, we propose two structured-knowledge incompatibility metrics, Entity Error Rate (EER) and Logical Inconsistency Rate (LIR), to quantify entity grounding and logical consistency for LLM-generated ontology definitions. We further develop an agentic quality-control (QC) workflow that treats definition generation as an iterative process rather than a direct decoding step: it generates definitions, extracts axioms, checks entity existence and logical consistency, and uses the resulting diagnostics to drive repair loops. Comprehensive experiments on Disease Ontology, Uberon Ontology, and Uberon-ConstraintStress demonstrate that EER and LIR complement conventional reference-based metrics by evaluating whether generated content can be grounded and checked inside the target ontology. The workflow effectively decreases EER while maintaining strong conventional text-generation performance. LIR further exposes sparse ontology-level logical failures that are invisible to text similarity metrics, although their repair remains limited.
Abstract: Biomedical ontologies are structured knowledge systems that must evolve continuously to represent newly emerging knowledge, but their manual maintenance remains time-consuming and laborintensive. Textual definitions are especially costly because they must be readable to humans and compatible with controlled entities, relations, and logical constraints. Large language models (LLMs) offer a promising way to assist ontology engineering tasks, including definition generation. However, textual plausibility does not guarantee knowledge-system compatibility. A generated definition may be fluent and close to a reference definition, yet still fail to ground its implied entities or violate ontology-level constraints. Directly inserting such definitions into ontology libraries may therefore introduce entity-level hallucinations and logical inconsistencies. To address this problem, we propose two structured-knowledge incompatibility metrics, Entity Error Rate (EER) and Logical Inconsistency Rate (LIR), to quantify entity grounding and logical consistency for LLM-generated ontology definitions. We further develop an agentic quality-control (QC) workflow that treats definition generation as an iterative process rather than a direct decoding step: it generates definitions, extracts axioms, checks entity existence and logical consistency, and uses the resulting diagnostics to drive repair loops. Comprehensive experiments on Disease Ontology, Uberon Ontology, and Uberon-ConstraintStress demonstrate that EER and LIR complement conventional reference-based metrics by evaluating whether generated content can be grounded and checked inside the target ontology. The workflow effectively decreases EER while maintaining strong conventional text-generation performance. LIR further exposes sparse ontology-level logical failures that are invisible to text similarity metrics, although their repair remains limited.
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From Fluent Text to Ontology-Compatible Definitions: A Quality-Control Agentic Workflow