BioMCP

A high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.

→ yeyuan98/biomcp-ts · listed on glama

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// key findings

⚠️

Known vulnerabilities in dependencies: 1 high

Affects packages this MCP installs at runtime. Upgrade or remove the affected dependency.

✅

25 tools verified — handlers match their declared behaviour

24 read-only tools verified — handlers contain no write/delete/exec

✅

No credential exfiltration, no sensitive file access, no obfuscation

Static analysis found nothing flowing your secrets to unexpected places.

✅

Open source with a license and README

Anyone can audit the code, the license is declared, and the publisher documents what it does.

🔐

You'll be asked for 8 credentials: ALPHAGENOME_API_KEY, DISGENET_API_KEY, GNOMAD_TOKEN, MYCHEM_API_KEY, NCBI_API_KEY, ONCOKB_TOKEN, S2_API_KEY, TEST_API_KEY

These are read from process.env at runtime. Make sure you trust where they’ll be sent.

// known CVEs in dependencies1 high1 low

Disclosed vulnerabilities in this server's declared npm dependencies (via OSV). Whether each is reachable depends on the installed versions.

highesbuild@0.28.0GHSA-gv7w-rqvm-qjhr

esbuild: Missing binary integrity verification in Deno module enables remote code execution via NPM_CONFIG_REGISTRY

lowesbuild@0.28.0GHSA-g7r4-m6w7-qqqr

esbuild allows arbitrary file read when running the development server on Windows

Depend on this server? Get alerted when its CVEs change.Watch this server free →

// required environment variables

This server reads these from process.env. You'll be asked to provide them before it can run.

🔐 secretALPHAGENOME_API_KEY— [AlphaGenome](https://www.alphagenome.com/) AlphaGenome variant scores

🔐 secretDISGENET_API_KEY— [DisGeNET](https://www.disgenet.org/) Disease-gene associations

🔐 secretGNOMAD_TOKEN

🔐 secretMYCHEM_API_KEY

🔐 secretNCBI_API_KEY— [NCBI](https://www.ncbi.nlm.nih.gov/account/settings/) Higher PubMed / NCBI rate limits

🔐 secretONCOKB_TOKEN— variant_oncokb Get OncoKB cancer variant annotations (requires )

🔐 secretS2_API_KEY— [Semantic Scholar API key](https://www.semanticscholar.org/product/api#api-key-form) (prevents 429 rate limits)

🔐 secretTEST_API_KEY

// full audit trail

The full breakdown of what we checked, the deductions that landed, the network hosts, the dependency advisories, and concrete fix guidance is available to verified publishers.

// improvement guidance — verified publishers only

We have 3 concrete improvements we can share with the publisher of this MCP. Each comes with specific guidance to raise the trust score.

// embed badge in your README

[![M8ven Score](https://m8ven.ai/badge/mcp/yeyuan98-biomcp-ts-1t6zfb)](https://m8ven.ai/mcp/yeyuan98-biomcp-ts-1t6zfb)

commit: 83bc278fee29796b501ea20a4536c05608def412

code hash: 132b4c245c527a3299e622d7390da44b44cfcd3ce2399269f31e3bb73895d25e

verified: 6/13/2026, 10:27:50 AM

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