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bioRxiv · 10.1101/2025.05.02.651919

BioMedTools: a language model-powered community for biomedical computational tools

Liu, S.·Xing, H.·Han, M.·Zhang, D.·Gong, L.·Liu, D.·Chen, J.·Cai, P.·Hu, Q.-N.
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Abstract

A large number of biomedical computational tools have spawned several tool registries. However, in the face of the rapid growth in the number of tools, existing tool registries, which are manually curated or community-driven, are difficult to keep up to date, resulting in inadequate tool repository data. In this paper, we show that language models (LMs) can aid in building a community of tools. We introduce BioMedTools (https://biomed.tools), a community of biomedical computational tools that mainly implements LM-based tool identification and a chat assistant. Compared with existing tool registries, BioMedTools achieves excellence in terms of the number of tools, frequency of data updates, and functionality. Meanwhile, the Model Context Protocol (MCP) servers hub in BioMedTools may promote the building of agents in the biomedical field. BioMedTools enables the efficient collection of tools and enhances their findability and accessibility.

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Liu, S., Xing, H., Han, M., Zhang, D., Gong, L., Liu, D., Chen, J., Cai, P., Hu, Q.-N.. 2025-05-08. BioMedTools: a language model-powered community for biomedical computational tools. https://doi.org/10.1101/2025.05.02.651919

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