biomcp-server

biomcp-server，来自 FreedomIntelligence/OpenClaw-Medical-Skills 的 agent 技能。

读凭据执行命令联网写文件严重 14 · 高危 67FreedomIntelligence/OpenClaw-Medical-Skills

它会碰到什么

扫了多少312 个文本文件，3520 KB

它会碰到什么读凭据执行命令联网写文件

命中总数422 处

命中统计严重 14 · 高 67 · 中 85 · 低 197

逐条看命中（30 条严重或高危）

严重 repo/docs/developer-guides/01-server-deployment.md:76cred-paths
```
# Create .env file
```
严重 repo/docs/developer-guides/01-server-deployment.md:77cred-paths
```
cat > .env << EOF
```
严重 repo/docs/developer-guides/01-server-deployment.md:102cred-paths
```
EnvironmentFile=/opt/biomcp/.env
```
严重 repo/docs/developer-guides/01-server-deployment.md:114persistence
```
sudo systemctl enable biomcp
```
严重 repo/docs/getting-started/01-quickstart-cli.md:29exec-pipe-to-shell
```
curl -LsSf https://astral.sh/uv/install.sh | sh
```
严重 repo/docs/getting-started/02-desktop-integration.md:35exec-pipe-to-shell
```
curl -LsSf https://astral.sh/uv/install.sh | sh
```
严重 repo/docs/getting-started/03-authentication-and-api-keys.md:229cred-paths
```
```
```
严重 repo/docs/getting-started/03-authentication-and-api-keys.md:230cred-paths
```
.env
```
严重 repo/docs/how-to-guides/04-predict-variant-effects-with-alphagenome.md:57cred-paths
```
# .env file
```
严重 repo/docs/troubleshooting.md:29exec-pipe-to-shell
```
curl -LsSf https://astral.sh/uv/install.sh | sh
```
严重 repo/docs/troubleshooting.md:39exec-pipe-to-shell
```
curl -LsSf https://astral.sh/uv/install.sh | sh
```

严重 repo/docs/troubleshooting.md:124persistence

echo 'export NCI_API_KEY="your-key-here"' >> ~/.bashrc

严重 repo/src/biomcp/__main__.py:17cred-paths
```
# Load environment variables from .env file
```
严重 repo/src/biomcp/cli/server.py:19cred-paths
```
# Load environment variables from .env file
```

高 README.md:36identity-config-write

Add to your `claude_desktop_config.json`:

高 repo/.github/actions/setup-python-env/action.yml:30exec-shell-true
```
shell: bash
```

高 repo/Dockerfile:8fs-destructive

RUN apt-get update && apt-get install -y --no-install-recommends gcc build-essential git && rm -rf /var/lib/apt/lists/*

高 repo/Dockerfile:27fs-destructive
```
rm -rf /tmp/alphagenome
```
高 repo/docs/faq-condensed.md:69fs-destructive
```
A: Clear with: `rm -rf ~/.biomcp/cache`
```

高 repo/docs/getting-started/02-desktop-integration.md:43identity-config-write

Add BioMCP to your application's configuration file (e.g., `claude_desktop_config.json` for Claude Desktop).

高 repo/docs/getting-started/02-desktop-integration.md:46identity-config-write

- **macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`

高 repo/docs/getting-started/02-desktop-integration.md:47identity-config-write
```
- **Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
```

高 repo/docs/troubleshooting.md:363identity-config-write

- macOS: `~/Library/Application Support/Claude/claude_desktop_config.json`

高 repo/docs/troubleshooting.md:364identity-config-write

- Windows: `%APPDATA%\Claude\claude_desktop_config.json`

高 repo/docs/troubleshooting.md:370identity-config-write

cat ~/Library/Application\ Support/Claude/claude_desktop_config.json | jq .

高 repo/docs/troubleshooting.md:391fs-destructive
```
- Clear cache: `rm -rf ~/.biomcp/cache`
```
高 repo/docs/troubleshooting.md:409fs-destructive
```
rm -rf ~/.biomcp/cache
```
高 repo/package-lock.json:1161identity-config-write
```
"node_modules/exit-hook": {
```
高 repo/scripts/generate_endpoints_doc.py:41exec-spawn
```
subprocess.run(  # noqa: S603
```

高 repo/src/biomcp/http_client_simple.py:115cred-envread

os.getenv("BIOMCP_USE_CONNECTION_POOL", "true").lower() == "true"

这一栏是扫描器报的事实，不是结论。命中多不等于有毒（安全工具、规则库、示例脚本本来就会包含危险写法），命中少也不等于干净。它和你手上的凭据、文件、网络有什么关系，需要你自己看。

技能内容

<!--

COPYRIGHT NOTICE

This file is part of the "Universal Biomedical Skills" project.

Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>

All Rights Reserved.

This code is proprietary and confidential.

Unauthorized copying of this file, via any medium is strictly prohibited.

Provenance: Authenticated by MD BABU MIA

-->

name: biomcp-server

description: MCP bio bridge

keywords:

MCP
PubMed
ClinicalTrials
server
uv

measurable_outcome: Stand up a working BioMCP endpoint (pip or uv) and return ≥1 PubMed + ≥1 ClinicalTrials.gov response to the client within 10 minutes.

license: MIT

metadata:

author: BioMCP Team

version: "1.0.0"

compatibility:

system: MCP-compliant clients

allowed-tools:

web_fetch

BioMCP Server

Deploy and operate the BioMCP server so MCP-compatible clients (Claude Desktop, LobeChat, etc.) can query biomedical databases via a single standardized interface.

When to Use

Unified literature search (PubMed/PMC) inside MCP clients.
Entity normalization via PubTator3 or genomic variant lookups.
ClinicalTrials.gov queries without bespoke API wrappers.

Core Capabilities

PubMed/PMC search: Execute complex literature queries.
PubTator3 annotations: Map text to genes, diseases, chemicals, species.
ClinicalTrials.gov: Retrieve trial metadata/protocols.
Genomic variant lookups: Fetch variant/gene summaries from connected sources.

Deployment Workflow

Install deps: cd repo && uv sync (preferred) or pip install ..
Run server: python -m biomcp.server or make run; Docker Compose provided.
Configure client: Add command/args snippet from README.md into MCP client config (Claude Desktop, BioKernel, etc.).
Test tools: Invoke PubMed + ClinicalTrials + variant endpoints to ensure connectivity.
Monitor: Capture logs, rate-limit statuses, and data-source versions for audit.

Guardrails

Keep API keys/env secrets outside the repo.
Respect upstream rate limits to avoid throttling or bans.
Document which data sources are enabled per deployment and update when they change.

References

Source repo + configuration examples in README.md, repo/docker-compose.yml, and repo/Makefile.

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去原始仓库

它属于哪个仓库

仓库FreedomIntelligence/OpenClaw-Medical-Skills

星标★ 3,010

本站分层T1

该仓技能数897

原文件路径skills/biomcp-server/SKILL.md

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