Medaka: Construction of Biomedical Knowledge Graphs Using Large Language Models

Asmita Sengupta, David Antony Selby, Sebastian Josef Vollmer, Gerrit Großmann

Keywords: Knowledge graph construction, Large language model, Information extraction

Abstract:

Knowledge graphs (KGs) are increasingly used to represent biomedical information in structured, interpretable formats. However, existing biomedical KGs often focus narrowly on molecular interactions or adverse events, overlooking the rich data found in drug leaflets.
In this work, we present (1) a hackable, end-to-end pipeline to create KGs from unstructured online content using a web scraper and an LLM; and (2) a curated dataset, Medaka, generated by applying this method to publicly available drug leaflets. The dataset captures clinically relevant attributes such as side effects, warnings, contraindications, ingredients, dosage guidelines, storage instructions and physical characteristics. We evaluate it through manual inspection and with an LLM-as-Judge framework, and compare its coverage with existing biomedical KGs and databases. We expect Medaka to support tasks such as patient safety monitoring and drug recommendation. The pipeline can also be used for constructing KGs from unstructured texts in other domains. Code and dataset are available at https://github.com/medaka25/medaka-25.

Primary Area: datasets and benchmarks

Submission Number: 8654