What features does BioMCP MCP server provide?

Q: What features does BioMCP MCP server provide?

Think Tool (Core): Critical first step for any biomedical task; enables sequential thinking, planning, and progress tracking (MCP think workflow).. Search Tool: Supports unified query language and domain-based searches, can return schema and explain how queries are parsed.. Fetch Tool: Retrieves full details for articles, trials, or variants with domain-specific detail options.. Comprehensive Tool Suite: Includes 24 specialized tools (articles, trials, variants, NCI tools, gene/disease/drug tools) for end-to-end biomedical queries.. MCP Transport & Compliance: Supports multiple transport modes (STDIO, worker SSE, streamable HTTP) with MCP compliance and a unified /mcp endpoint.. Deployment & Scaling: Docker-based deployment and Cloudflare Workers option for cloud-scale hosting.. Environment & Configuration: Optional tokens and tuning via environment variables (CBIO_TOKEN, ONCOKB_TOKEN, connection pooling, metrics).. Certification & Enterprise: MCPHub-certified with OncoMCP enterprise offering HIPAA-compliant deployment and expanded oncology data.

BioMCP MCP Server 2025: Features & Setup Guide

Overview

BioMCP (Biomedical Model Context Protocol) is an MIT-licensed open source toolkit that equips AI assistants with specialized biomedical knowledge. Built around the Model Context Protocol, it provides structured access to clinical trials, literature, and genomic data by connecting AI systems to authoritative sources such as PubMed/PubTator3, Europe PMC, ClinicalTrials.gov, NCI CTS API, BioThings suite (MyVariant.info, MyGene.info, MyDisease.info, MyChem.info), TCGA/GDC, 1000 Genomes, cBioPortal, and OncoKB demo. The server exposes 24 tools (3 core: think, search, fetch; plus 21 domain tools) for end-to-end literature, trial, and variant queries. It supports a CLI and multiple transport modes (STDIO for local development, HTTP streamable and worker modes for server deployment), with Docker and Cloudflare Workers deployment options. It includes environment variables for optional authentication tokens (CBIO, OncoKB) and performance metrics. It is MCPHub-certified, and offers an enterprise version OncoMCP with HIPAA-compliant deployment and expanded knowledge base. The README provides example use cases and extensive documentation, making BioMCP suitable for AI-assisted biomedical research workflows via a consistent MCP interface.

Features

Think Tool (Core)

Critical first step for any biomedical task; enables sequential thinking, planning, and progress tracking (MCP think workflow).

Search Tool

Supports unified query language and domain-based searches, can return schema and explain how queries are parsed.

Fetch Tool

Retrieves full details for articles, trials, or variants with domain-specific detail options.

Comprehensive Tool Suite

Includes 24 specialized tools (articles, trials, variants, NCI tools, gene/disease/drug tools) for end-to-end biomedical queries.

MCP Transport & Compliance

Supports multiple transport modes (STDIO, worker SSE, streamable HTTP) with MCP compliance and a unified /mcp endpoint.

Deployment & Scaling

Docker-based deployment and Cloudflare Workers option for cloud-scale hosting.

Environment & Configuration

Optional tokens and tuning via environment variables (CBIO_TOKEN, ONCOKB_TOKEN, connection pooling, metrics).

Certification & Enterprise

MCPHub-certified with OncoMCP enterprise offering HIPAA-compliant deployment and expanded oncology data.