BioMCP-TS

io.github.yeyuan98/biomcp-tsv0.9.0Other

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

The current version, v0.9.0, was published to the official MCP registry on 2026-08-31. It is distributed as biomcp on npm, filed under Other by this index, and declares 8 environment variables. Removals and unreachable sources are measured across every server this index tracks, contract drift across the servers that answer in consecutive snapshots; the index's current counts put this record in context.

In-path gate · all MCP tools

Using BioMCP-TS in Claude, Cursor, Gemini CLI, Cline, or Zed?

MCP tool contracts can change remotely with no version bump. The mcpindex gate pins each contract and HOLDs the call when it drifts-before your agent acts. Zero credentials. This is not the package install for this server itself (use Install this server for that).

Install the mcpindex gate (one command)

Rewrites your MCP host config so each server launches behind the gate. Inspect first: curl -fsSL https://mcpindex.ai/install.sh | less

uv tool install mcpindex-gate && mcpindex-config-wire

Auditable install path →Watch it hold a drift →

Trust verdict · v1 advisory · method

NOT YET SCREENEDno verdict on file

Verdict not yet evaluated for this tool. The semantic screen takes adversarial cases first; coverage rolls out as the corpus expands (15/150 labels to graduation). The deterministic conformance probe is built but has not yet run on the public corpus, so a recorded verdict here is REVIEW or UNVERIFIED, never a clearing ALLOW. Until a verdict is recorded, an agent should treat this tool as not-yet-cleared and fall back to its own checks. Method: the eval, four-state verdict, honest limits.

Own this server? Screen its description →

That verdict was true at screening time (snapshot 2026-08-31).

Contracts can change after screening, with no version bump. The gate pins BioMCP-TS’s tool contracts on first sight and holds any silent change before your agent acts - the check that keeps being true on Tuesday.

See your first HOLD in 2 minutes →

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

MCP quality score · maturity, not trust · methodology

freshness

completeness

installability

documentation

stability

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Install this server

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "--",
        "biomcp"
      ],
      "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>"
      }
    }
  }
}

Cursor (.cursor/mcp.json)

{
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "--",
        "biomcp"
      ],
      "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>"
      }
    }
  }
}

Cline (cline_mcp_settings.json)

npx -y -- biomcp

Claude Code (claude mcp add)

claude mcp add --scope user biomcp-ts -- npx -y -- biomcp

Gemini CLI (gemini mcp add)

gemini mcp add -s user biomcp-ts npx -y -- biomcp

Verdict API

curl -s mcpindex.ai/api/v1/trust/server/io-github-yeyuan98-biomcp-ts

Free-tier verdict as JSON: decision + dimensions + severity. Call it from your agent before it invokes a tool it just discovered.

Details

version: v0.9.0
category: Other
quality: 90 / 100
operator: yeyuan98

Listing

Listed from the official MCP registry. Unclaimed by its maintainer. Maintainer? Email us →

Provenance

Each verdict is bound to a hash of the exact description it judged, so a re-crawl that changes the text produces a new record rather than silently inheriting this one. Verdict history is hash-chained and anchored to Bitcoin via OpenTimestamps (latest confirmed at block 964,828). Verify it yourself.

Links

Repository →Website →