MCPmed: A Call for MCP-Enabled Bioinformatics Web Services for LLM-Driven Discovery
Journal:
arXiv
Published Date:
Jul 10, 2025
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 human-centric
design limits machine readability for large language models (LLMs) and deep
research agents. We address this gap by adapting the Model Context Protocol
(MCP) to bioinformatics web server backends - a standardized,
machine-actionable layer that explicitly associates webservice endpoints with
scientific concepts and detailed metadata. Our implementations across
widely-used databases (GEO, STRING, 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 significantly enhances automation, reproducibility,
and interoperability, preparing bioinformatics web services for next-generation
research agents.
