BioMCP

BioMCP provides a unified command interface for querying and analyzing data from a wide range of biomedical sources. Designed for researchers, clinicians, and agents, the tool aims to streamline the process of accessing and cross-referencing biomedical information by consolidating searches, detail retrieval, and cross-entity pivots into a single workflow. It addresses the challenge of navigating multiple database sites, authentication schemes, and API documentation by offering a consistent command grammar for interacting with trusted biomedical data sources.

The platform supports searching for articles, genes, variants, drugs, diseases, pathways, proteins, and more, with the ability to pivot between related entities such as moving from a gene to associated trials or drugs. BioMCP enables gene-set enrichment analysis and local study analytics on downloaded cBioPortal datasets, enhancing its analytical capabilities. It also features workflows for annotating variants, predicting effects, and reproducing research papers, as well as generating a variety of study charts including bar, pie, scatter, heatmap, and survival plots. The search functionality can deduplicate identifiers across sources like PubTator3 and Europe PMC, and can incorporate Semantic Scholar data when applicable.

BioMCP is delivered as a command-line tool, installable via binary or PyPI (biomcp-cli), and can be run locally or as a remote HTTP server for shared deployments. It integrates with MCP clients such as Claude Desktop, Cursor, VS Code, and others that accept mcpServers JSON. Users can install guided investigation workflows, referred to as "skills," to extend its capabilities within agent directories. The tool also provides API keys for access management and supports skill authoring and validation for custom workflows.