HERMES: a multi-agent framework for structured knowledge extraction from ultra-long documents in geoscience

Abstract

Authoritative scientific knowledge in geoscience remains largely trapped in legacy monographs and historical literature, where unstructured text and complex layouts hinder computational access. We introduce HERMES, a scalable multi-agent framework that extracts structured data from ultra-long scientific documents. Using a coordinating large language model, HERMES integrates domain constraints, validation rules and evidence tracing within a unified document-level extraction process that incorporates parsed text, tables, figures and captions. Applied to the 55-volume Treatise on Invertebrate Paleontology, the system produced a structured database of 32,277 fossil taxonomic entities and 451,878 attributes, released online at https://treatise.geolex.org. Extraction performance remained stable across fossil groups (average F1 scores of approximately 0.90 for entities and 0.91 for attributes), improving per-volume efficiency approximately sixfold relative to the tested fully manual baseline. Evaluation in palaeomagnetism and geochemistry, conducted without additional model training, demonstrated transfer across distinct geoscience domains. This work provides a practical pathway to transform historical scientific literature into FAIR-oriented structured data, offering a sustainable infrastructure for data-intensive disciplines and large-scale knowledge integration.