biomcp and knowledgebase-mcp
These are ecosystem siblings—BioMCP provides a standardized protocol framework for biomedical AI integration, while BioContextAI's server implements that protocol as a specific knowledge base instance that can be plugged into MCP-compatible applications.
About biomcp
genomoncology/biomcp
BioMCP: Biomedical Model Context Protocol
Implements a unified CLI and MCP server that federates queries across 20+ biomedical APIs (PubMed, ClinVar, UniProt, cBioPortal, etc.) with a single grammar—`search`, `get`, and cross-entity pivots eliminate API-specific syntax. Supports local study analytics (cohort, survival, co-occurrence) from cBioPortal datasets with native SVG/PNG charts, plus progressive disclosure via composable sections and batch enrichment via g:Profiler. Deploys as a standalone binary, PyPI tool, Claude Desktop MCP server, or remote HTTP service with automatic reconnection and health probes.
About knowledgebase-mcp
biocontext-ai/knowledgebase-mcp
BioContextAI Knowledgebase MCP server for biomedical agentic AI
Implements unified MCP access to 14+ biomedical databases (PubMed, STRING, AlphaFold, KEGG, Reactome, etc.), enabling LLMs to query gene annotations, literature, protein interactions, and pathway data through standardized tools. Supports flexible deployment via stdio transport for Claude Desktop/IDEs, HTTP with uvicorn for remote use, or Docker, with extensible OpenAPI integration for custom data sources via configuration.
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