BioMCP-TS MCP Server

by yeyuan98io.github.yeyuan98/biomcp-tsv1.4.3

Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.

12Node.jsstdioofficial registry

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Active12d ago

Install BioMCP-TS MCP server

claude mcp add bio -e NCBI_API_KEY='<ncbi-api-key>' -e S2_API_KEY='<s2-api-key>' -e OPENFDA_API_KEY='<openfda-api-key>' -e ONCOKB_TOKEN='<oncokb-token>' -e DISGENET_API_KEY='<disgenet-api-key>' -- npx -y biomcp

{
  "mcpServers": {
    "bio": {
      "command": "npx",
      "args": [
        "-y",
        "biomcp"
      ],
      "env": {
        "NCBI_API_KEY": "<ncbi-api-key>",
        "S2_API_KEY": "<s2-api-key>",
        "OPENFDA_API_KEY": "<openfda-api-key>",
        "ONCOKB_TOKEN": "<oncokb-token>",
        "DISGENET_API_KEY": "<disgenet-api-key>"
      }
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project).

{
  "mcpServers": {
    "bio": {
      "command": "npx",
      "args": [
        "-y",
        "biomcp"
      ],
      "env": {
        "NCBI_API_KEY": "<ncbi-api-key>",
        "S2_API_KEY": "<s2-api-key>",
        "OPENFDA_API_KEY": "<openfda-api-key>",
        "ONCOKB_TOKEN": "<oncokb-token>",
        "DISGENET_API_KEY": "<disgenet-api-key>"
      }
    }
  }
}

Settings → Developer → Edit Config (claude_desktop_config.json), then restart.

{
  "servers": {
    "bio": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "biomcp"
      ],
      "env": {
        "NCBI_API_KEY": "<ncbi-api-key>",
        "S2_API_KEY": "<s2-api-key>",
        "OPENFDA_API_KEY": "<openfda-api-key>",
        "ONCOKB_TOKEN": "<oncokb-token>",
        "DISGENET_API_KEY": "<disgenet-api-key>"
      }
    }
  }
}

Add to .vscode/mcp.json in your workspace.

{
  "mcpServers": {
    "bio": {
      "command": "npx",
      "args": [
        "-y",
        "biomcp"
      ],
      "env": {
        "NCBI_API_KEY": "<ncbi-api-key>",
        "S2_API_KEY": "<s2-api-key>",
        "OPENFDA_API_KEY": "<openfda-api-key>",
        "ONCOKB_TOKEN": "<oncokb-token>",
        "DISGENET_API_KEY": "<disgenet-api-key>"
      }
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json.

Configuration

Variable	Required	Secret	Description
ANALYSIS_BIOWASM	—	—	Set to 1 to enable the samtools/bedtools/bcftools biowasm analysis tools
ANALYSIS_R	—	—	Set to 1 to enable the R/Bioconductor analysis tools (requires the webr peer dependency; use the pinned one-shot client command)
DB_TYPE	—	—	Set to mysql or sqlite to enable the read-only SQL database tools
NCBI_API_KEY	—	yes	Higher NCBI E-utilities rate limits (3 -> 10 req/s)
S2_API_KEY	—	yes	Higher Semantic Scholar rate limits
OPENFDA_API_KEY	—	yes	Higher OpenFDA rate limits
ONCOKB_TOKEN	—	yes	Required by the variant_oncokb tool (OncoKB annotations)
DISGENET_API_KEY	—	yes	Required for DisGeNET disease-gene associations

Freshness

Active — last maintenance signal 12d ago. The newest of the signals below sets the band.

Last commit (default branch)
2026-09-28 · 12d ago · GitHub
Latest release
2026-09-19 · 20d ago · GitHub · v1.5.0
Package published
no data · npm/PyPI
Registry entry updated
2026-09-14 · 26d ago · official registry · v1.4.3

FAQ

›How do I install the BioMCP-TS MCP server in Claude Code?

Run: claude mcp add bio -e NCBI_API_KEY='<ncbi-api-key>' -e S2_API_KEY='<s2-api-key>' -e OPENFDA_API_KEY='<openfda-api-key>' -e ONCOKB_TOKEN='<oncokb-token>' -e DISGENET_API_KEY='<disgenet-api-key>' -- npx -y biomcp. For Cursor, VS Code, Claude Desktop and Windsurf, use the install tabs above.

›Does BioMCP-TS require an API key?

Yes. It expects NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY, of which 5 are secrets.

›Can I use BioMCP-TS as a remote (hosted) MCP server?

No hosted endpoint is published; it runs locally over stdio.

›Is BioMCP-TS in the official MCP registry?

Yes, as io.github.yeyuan98/biomcp-ts.