A novel pipeline for the rapid expansion of ecological trait databases using LLMs

Ramos, R. J.; Afkhami, M. E.; Aguilar-Trigueros, C. A.; Barbour, K. M.; Chaverri, P.; Cuprewich, S. A.; Egan, C. P.; Lynn, K. M. T.; Peay, K. G.; Norros, V.; Romero-Olivares, A. L.; Ward, L.; Chaudhary, B.

doi:10.64898/2026.03.10.710865

bioRxiv · 10.64898/2026.03.10.710865

A novel pipeline for the rapid expansion of ecological trait databases using LLMs

Ramos, R. J.·Afkhami, M. E.·Aguilar-Trigueros, C. A.·Barbour, K. M.·Chaverri, P.·Cuprewich, S. A.·Egan, C. P.·Lynn, K. M. T.·Peay, K. G.·Norros, V.·Romero-Olivares, A. L.·Ward, L.·Chaudhary, B.

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Abstract

This paper presents a novel workflow leveraging Large Language Models (LLMs) to rapidly extract trait data from fungal species descriptions, addressing a significant bottleneck in ecological research. We developed and evaluated an LLM pipeline to extract morphological trait data from arbuscular mycorrhizal fungi, comparing performance against a manually curated dataset (TraitAM). Results demonstrate the potential of LLMs for automated trait data acquisition, though accuracy varies by trait and model, with systematic biases observed. This framework offers a blueprint for building trait databases across diverse taxa and domains, significantly accelerating ecological research and conservation efforts.

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Ramos, R. J., Afkhami, M. E., Aguilar-Trigueros, C. A., Barbour, K. M., Chaverri, P., Cuprewich, S. A., Egan, C. P., Lynn, K. M. T., Peay, K. G., Norros, V., Romero-Olivares, A. L., Ward, L., Chaudhary, B.. 2026-03-12. A novel pipeline for the rapid expansion of ecological trait databases using LLMs. https://doi.org/10.64898/2026.03.10.710865

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