生物医学模型

Installation

Binary install

curl -fsSL https://biomcp.org/install.sh | bash

PyPI tool install

```bash uv tool install biomcp-cli

or: pip install biomcp-cli

```

PyPI package warning: install biomcp-cli, not biomcp. The biomcp PyPI package is unrelated to this project.

MCP Registry ownership marker: mcp-name: io.github.genomoncology/biomcp.

This installs the biomcp binary in ~/.local/bin. If that directory is not already on PATH, the installer prints one command to add it; it never edits your shell startup files.

Docker

docker run --rm ghcr.io/genomoncology/biomcp --version
docker run --rm ghcr.io/genomoncology/biomcp list
docker run --rm -i ghcr.io/genomoncology/biomcp serve

Use the GHCR image for quick CLI checks or stdio MCP clients without a local install.

Install skills

Install guided investigation workflows into your agent directory:

biomcp skill install ~/.claude --force

Multi-worker deployment

BioMCP rate limiting is process-local. For many concurrent workers, run one shared Streamable HTTP biomcp serve-http endpoint so all workers share a single limiter budget:

biomcp serve-http --host 0.0.0.0 --port 8080 \
  --allowed-hosts biomcp.example.org

Loopback servers accept only local Host values by default. A non-loopback bind requires --allowed-hosts. The explicit --unsafe-allow-any-host escape hatch disables only this Host check; it does not add authentication, TLS, or encryption. Put remote deployments behind a trusted authenticated TLS proxy or inside a private network.

Remote clients should connect to http://<host>:8080/mcp. Lightweight process probes are available at GET /health, GET /readyz, and GET /.

Quick start

First useful query in under 30 seconds:

uv tool install biomcp-cli
biomcp health --apis-only
biomcp skill list
biomcp list gene
biomcp search all --gene BRAF --disease melanoma  # unified cross-entity discovery
biomcp get gene BRAF pathways hpa

Usage Examples

Credentialed OncoKB example

User prompt: Show OncoKB therapy evidence for BRAF V600E.

Expected tool call: biomcp variant oncokb "BRAF V600E"

Expected behavior: Uses ONCOKB_TOKEN when configured and otherwise returns helpful guidance about the missing credential.

Expected output: Therapy and level evidence when ONCOKB_TOKEN is set, or a clear setup hint when it is not.

Credentialed DisGeNET example

User prompt: Show scored DisGeNET associations for TP53.

Expected tool call: biomcp get gene TP53 disgenet

Expected behavior: Uses DISGENET_API_KEY to retrieve the scored gene-disease association section.

Expected output: Ranked disease-association table with evidence counts and scores when DISGENET_API_KEY is configured.

Configuration

Claude Desktop extension settings

The directory bundle exposes only the optional settings needed for the first reviewer-facing build:

The first directory build exposes only those three optional settings. Advanced CLI-only env vars remain documented in API Keys for the general BioMCP CLI path.

API keys

Most commands work without credentials. Optional keys improve rate limits or unlock optional enrichments:

export NCBI_API_KEY="..."        # ClinVar, PubTator, PubMed/efetch, PMC OA, NCBI ID converter
export S2_API_KEY="..."          # Optional Semantic Scholar auth; dedicated quota at 1 req/sec
export OPENFDA_API_KEY="..."     # OpenFDA rate limits
export NCI_API_KEY="..."         # NCI CTS trial search (--source nci)
export ONCOKB_TOKEN="..."        # OncoKB variant helper
export ALPHAGENOME_API_KEY="..." # AlphaGenome variant effect prediction

search article, get article, article batch, get article ... tldr, and the explicit Semantic Scholar helpers all work without S2_API_KEY. With the key, BioMCP sends authenticated requests and uses a dedicated rate limit at 1 req/sec. Without it, BioMCP uses the shared unauthenticated pool at 1 req/2sec. search article --source supports all, pubtator, europepmc, pubmed, semanticscholar, and litsense2. The default compatible article federation uses PubTator3, Europe PMC, PubMed, and automatic Semantic Scholar; use --source semanticscholar or --source litsense2 explicitly when you want one of those sources alone. Explicit source selection also disables cross-provider row enrichment. References and recommendations can be empty for paywalled papers because of publisher elision in Semantic Scholar upstream coverage.

Claude Code plugin

Install the biomcp binary first, then add the hosted plugin marketplace and install the BioMCP plugin in Claude Code:

/plugin marketplace add genomoncology/biomcp
/plugin install biomcp@biomcp

The plugin wires Claude Code to the local stdio MCP server with biomcp serve. For guided BioMCP workflows, also install the skill assets below.

Claude Desktop extension (.mcpb)

Install BioMCP from the Anthropic Directory in Claude Desktop when that path is available for your environment. For local/manual setups, use the JSON MCP config below.