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bioRxiv · 10.64898/2026.06.16.732577

VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase

McLachlan, A. D.·Court, R.·Pilgrim, C.·Longden, K.·Brown, N. H. D.·Osumi-Sutherland, D.·Jefferis, G. S. X. E.·Armstrong, D. J.
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Abstract

Biological databases store curated knowledge that researchers traditionally access through web interfaces or APIs. To move beyond casual browsing requires domain-specific knowledge and expertise to frame the queries necessary to explore this data. This generates barriers to both experienced users trying to integrate wide-ranging sources of information and for new users entering scientific fields undergoing paradigm shifts such as connectomics. A potentially powerful method to lower these barriers is to facilitate natural-language access to these databases by exposing them to large language models (LLMs) via the Model Context Protocol (MCP). Here we implement this for Virtual Fly Brain (VFB), an expert-curated and ontology-backed knowledgebase of Drosophila neuroscience, providing the precision needed to make recently integrated connectome and molecular data accessible. Benchmarked on 30 neuroscience tasks against a bare LLM and a web-search-assisted LLM, the VFB-MCP-equipped LLM produces precise, verifiable and appropriately quantified answers on 25/30 tasks vs 14/30 for web and 2/30 for bare. The MCP advantage is largest for tasks where data quantification is required (89% vs 11% web). This work establishes MCP layered over ontology-backed knowledge graphs as an effective method to improve LLM response quality for neuroscience and connectomics data, promoting accessibility and accelerating the reliable analysis of complex integrated datasets.

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McLachlan, A. D., Court, R., Pilgrim, C., Longden, K., Brown, N. H. D., Osumi-Sutherland, D., Jefferis, G. S. X. E., Armstrong, D. J.. 2026-06-21. VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase. https://doi.org/10.64898/2026.06.16.732577

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