Automated Standardization of Legacy Biomedical Metadata Using an Ontology-Constrained LLM Agent

Computer Science > Databases [Submitted on 10 Mar 2026 (v1), last revised 18 Jun 2026 (this version, v2)] Title:Automated Standardization of Legacy Biomedical Metadata Using an Ontology-Constrained LLM Agent View PDFAbstract:Scientific metadata are often incomplete and noncompliant with community standards, limiting dataset findability, interoperability, and reuse. Even when standard metadata reporting guidelines exist, they typically lack machine-actionable representations. Producing FAIR datasets requires encoding metadata standards as machine-actionable templates with rich field specifications and precise value constraints. Recent work has shown that LLMs guided by field names and ontology constraints can improve metadata standardization, but these approaches treat constraints as static text prompts, relying on the model's training knowledge alone. We present an LLM-based metadata standardization system that queries standard reporting guidelines and authoritative biomedical terminology services in real time to retrieve canonically correct standards on demand. We evaluate this approach on 839 legacy metadata records from the Human BioMolecular Atlas Program (HuBMAP) using an expert-curated gold standard for exact-match assessment. Our evaluation shows that augmenting the LLM with real-time tool access consistently improves prediction accuracy over the LLM alone across both ontology-constrained and non-ontology-constrained fields, demonstrating a practical approach to automated standardization of biomedical metadata. Submission history From: Josef Hardi [view email][v1] Tue, 10 Mar 2026 18:47:30 UTC (529 KB) [v2] Thu, 18 Jun 2026 17:56:13 UTC (960 KB) References & Citations Loading... Bibliographic and Citation Tools Bibliographic Explorer (What is the Explorer?) Connected Papers (What is Connected Papers?) Litmaps (What is Litmaps?) scite Smart Citations (What are Smart Citations?) Code, Data and Media Associated with this Article alphaXiv (What is alphaXiv?) CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub (What is DagsHub?) Gotit.pub (What is GotitPub?) Hugging Face (What is Huggingface?) ScienceCast (What is ScienceCast?) Demos Recommenders and Search Tools Influence Flower (What are Influence Flowers?) CORE Recommender (What is CORE?) arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.