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Updated: Feb 25, 2026

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

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MCPmed: una llamada a servicios web de bioinformática habilitados para el Protocolo de Contexto de Modelo para el

Matthias Flotho^1,2, Ian Ferenc Diks^1,2, Philipp Flotho¹

¹Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, Saarland University Campus, 66123 Saarland, Germany.

Briefings in bioinformatics

|February 23, 2026

Abstract:

Bioinformatics web servers are critical resources in modern biomedical research, facilitating interactive exploration of datasets through custom-built interfaces with rich visualization capabilities. However, this mostly human-centric design limits machine readability for large language models (LLMs) and deep research agents. We address this gap by adapting model context protocol (MCP) to bioinformatics web server backends, a standardized, machine-actionable layer that explicitly associates web service endpoints with scientific concepts and detailed metadata. Our implementations across widely used databases (GEO, STRING, and UCSC Cell Browser) demonstrate enhanced exploration capabilities through MCP-enabled LLMs. To accelerate adoption, we propose MCPmed, a community effort supplemented by lightweight breadcrumbs for services not yet fully MCP-enabled and templates for setting up new servers. This structured transition aims to significantly enhance automation, reproducibility, and interoperability, preparing bioinformatics web services for next-generation research agents.

Palabras clave:

API GEO LLM MCP base de datos servidor web

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