Application of Large Language Models for Annotating Genes into Reactome Pathways

Wu, G.; Matthews, L.; Boyer, N.; Milacic, M.; Beavers, D.; Li, N. T.; May, B.; Rothfels, K.; Shamovsky, V.; Stephan, R.; Gillespie, M.; Hermjakob, H.; DEustachio, P.; Stein, L. D.

doi:10.64898/2025.12.20.695723

bioRxiv · 10.64898/2025.12.20.695723

Application of Large Language Models for Annotating Genes into Reactome Pathways

Wu, G.·Matthews, L.·Boyer, N.·Milacic, M.·Beavers, D.·Li, N. T.·May, B.·Rothfels, K.·Shamovsky, V.·Stephan, R.·Gillespie, M.·Hermjakob, H.·DEustachio, P.·Stein, L. D.

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Abstract

Reactome is the most comprehensive, open source, open access biological pathway knowledgebase, widely used in the research community. To ensure the highest quality of its content, human pathway data in Reactome is manually curated. However, manual curation is labor-intensive, time-consuming, and increasingly difficult to keep up with the ever-growing biomedical literature. Large language model (LLM)-driven artificial intelligence (AI) technologies are transforming many fields, including bioinformatics resource development. Applying LLM/AI technologies in Reactome may offer a powerful way to scale curation and consolidate pathway-related data into a single resource. This manuscript describes the first stage of our attempt to adopt LLM/AI technologies for Reactome manual curation. We developed an LLM workflow that can assist curators in adding new genes to existing pathways and refining the functional annotations of existing ones. The workflow predicts pathways in which genes are likely to function, identifies PubMed-indexed literature that may support these predictions, generates text summaries describing potential molecular mechanisms, and extracts functional relationships among biological entities from full-text PDF papers. To validate the workflow output, we used a computational approach based on semantic similarity between LLM workflow-generated summaries and Reactome manual annotations. The results show significant enrichment of high-similarity matches. Manual evaluation of 19 genes indicated that more than half of the outputs are useful for supporting curation. Based on these results, we developed an enhanced workflow that incorporates protein-protein interaction data, facilitating Reactomes reaction-based annotation. In summary, our initial adoption of LLM/AI technologies produced encouraging results and provides a practical framework for integrating AI-assisted methods into Reactomes curation pipeline. The strategies described here may be broadly applicable to community knowledgebases in general.

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Wu, G., Matthews, L., Boyer, N., Milacic, M., Beavers, D., Li, N. T., May, B., Rothfels, K., Shamovsky, V., Stephan, R., Gillespie, M., Hermjakob, H., DEustachio, P., Stein, L. D.. 2025-12-23. Application of Large Language Models for Annotating Genes into Reactome Pathways. https://doi.org/10.64898/2025.12.20.695723

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