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BioMCP-TS

Official registry Data and databases

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

Source code Website

Install

Add this to your client's MCP configuration (Claude Desktop: claude_desktop_config.json; Cursor: .cursor/mcp.json; VS Code and others use the same "mcpServers" shape).

NPM package biomcp
Claude Code 
claude mcp add biomcp-ts -e 'ANALYSIS_BIOWASM=<ANALYSIS_BIOWASM>' -e 'ANALYSIS_R=<ANALYSIS_R>' -e 'DB_TYPE=<DB_TYPE>' -e 'NCBI_API_KEY=<your ncbi_api_key>' -e 'S2_API_KEY=<your s2_api_key>' -e 'OPENFDA_API_KEY=<your openfda_api_key>' -e 'ONCOKB_TOKEN=<your oncokb_token>' -e 'DISGENET_API_KEY=<your disgenet_api_key>' -- npx -y biomcp@1.4.3
JSON configuration (Claude Desktop, Cursor, VS Code) 
{
    "mcpServers": {
        "biomcp-ts": {
            "command": "npx",
            "args": [
                "-y",
                "biomcp@1.4.3"
            ],
            "env": {
                "ANALYSIS_BIOWASM": "<ANALYSIS_BIOWASM>",
                "ANALYSIS_R": "<ANALYSIS_R>",
                "DB_TYPE": "<DB_TYPE>",
                "NCBI_API_KEY": "<your ncbi_api_key>",
                "S2_API_KEY": "<your s2_api_key>",
                "OPENFDA_API_KEY": "<your openfda_api_key>",
                "ONCOKB_TOKEN": "<your oncokb_token>",
                "DISGENET_API_KEY": "<your disgenet_api_key>"
            }
        }
    }
}

Environment variables

  • 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 secret Higher NCBI E-utilities rate limits (3 -> 10 req/s)
  • S2_API_KEY secret Higher Semantic Scholar rate limits
  • OPENFDA_API_KEY secret Higher OpenFDA rate limits
  • ONCOKB_TOKEN secret Required by the variant_oncokb tool (OncoKB annotations)
  • DISGENET_API_KEY secret Required for DisGeNET disease-gene associations

Frequently asked questions

What is BioMCP-TS?

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

How do I install BioMCP-TS?

It runs on your machine. In Claude Code: claude mcp add biomcp-ts -e 'ANALYSIS_BIOWASM=<ANALYSIS_BIOWASM>' -e 'ANALYSIS_R=<ANALYSIS_R>' -e 'DB_TYPE=<DB_TYPE>' -e 'NCBI_API_KEY=<your ncbi_api_key>' -e 'S2_API_KEY=<your s2_api_key>' -e 'OPENFDA_API_KEY=<your openfda_api_key>' -e 'ONCOKB_TOKEN=<your oncokb_token>' -e 'DISGENET_API_KEY=<your disgenet_api_key>' -- npx -y biomcp@1.4.3. For other clients, paste the JSON configuration from this page into their MCP settings.

Does BioMCP-TS need an API key?

Yes. It expects NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY, which you set in its configuration.

Is BioMCP-TS open source?

Its code is public on GitHub, but the repository does not declare a standard license.

Who maintains BioMCP-TS?

It is published by yeyuan98. AI.tn lists it but does not maintain or endorse it.

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