Identifying Biomedical Entities for Datasets in Scientific Articles: 4-Step Cache-Augmented Generation Approach Using GPT-4o and PubTator 3.0.

Background: The accurate extraction of biomedical entities in scientific articles is essential for effective metadata annotation of research datasets, ensuring data findability, accessibility, interoperability, and reusability in collaborative research. Objective: This study aimed to introduce a novel 4-step cache-augmented generation approach to identify biomedical entities for an automated metadata annotation of datasets, leveraging GPT-4o and PubTator 3.0. Methods: The method integrates four steps: (1) generation of candidate entities using GPT-4o, (2) validation via PubTator 3.0, (3) term extraction based on a metadata schema developed for the specific research area, and (4) a combined evaluation of PubTator-validated and schema-related terms. Applied to 23 articles published in the context of the Collaborative Research Center OncoEscape, the process was validated through supervised, face-to-face interviews with article authors, allowing an assessment of annotation precision using random-effects meta-analysis. Results: The approach yielded a mean of 19.6 schema-related and 6.7 PubTator-validated biomedical entities per article. Within the study's specific context, the overall annotation precision was 98% (95% CI 94%-100%), with most prediction errors concentrated in articles outside the primary basic research domain of the schema. In a subsample (n=20), available supplemental material was included in the prediction process, but it did not improve precision (98%, 95% CI 95%-100%). Moreover, the mean number of schema-related entities was 20.1 (P=.56) and the mean number of PubTator-validated entities was 6.7 (P=.68); these values did not increase with the additional information provided in the supplement. Conclusions: This study highlights the potential of large language model-supported metadata annotation. The findings underscore the practical feasibility of full-text analysis and suggest its potential for integration into routine workflows for biomedical metadata generation.