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8 clients · secrets stay placeholders

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

claude mcp add biomcp-ts -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 [email protected]

[mcp_servers.biomcp-ts]
command = "npx"
args = ["-y", "[email protected]"]
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}" }

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "biomcp-ts": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "[email protected]"
      ],
      "enabled": true,
      "environment": {
        "NCBI_API_KEY": "{env:NCBI_API_KEY}",
        "S2_API_KEY": "{env:S2_API_KEY}",
        "OPENFDA_API_KEY": "{env:OPENFDA_API_KEY}",
        "ONCOKB_TOKEN": "{env:ONCOKB_TOKEN}",
        "DISGENET_API_KEY": "{env:DISGENET_API_KEY}"
      }
    }
  }
}

{
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "[email protected]"
      ],
      "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}"
      }
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=biomcp-ts&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsImJpb21jcEAxLjQuMyJdLCJlbnYiOnsiTkNCSV9BUElfS0VZIjoiJHtOQ0JJX0FQSV9LRVl9IiwiUzJfQVBJX0tFWSI6IiR7UzJfQVBJX0tFWX0iLCJPUEVORkRBX0FQSV9LRVkiOiIke09QRU5GREFfQVBJX0tFWX0iLCJPTkNPS0JfVE9LRU4iOiIke09OQ09LQl9UT0tFTn0iLCJESVNHRU5FVF9BUElfS0VZIjoiJHtESVNHRU5FVF9BUElfS0VZfSJ9fQ%3D%3D"
}

{
  "servers": {
    "biomcp-ts": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "[email protected]"
      ],
      "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}"
      }
    }
  }
}

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

extensions:
  "biomcp-ts":
    enabled: true
    name: "biomcp-ts"
    type: stdio
    cmd: "npx"
    args:
      - "-y"
      - "[email protected]"
    envs:
      "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}"
    timeout: 300

Placeholders to fill from your own secret store: ${NCBI_API_KEY}, ${S2_API_KEY}, ${OPENFDA_API_KEY}, ${ONCOKB_TOKEN}, ${DISGENET_API_KEY}. The registry never accepts secret values.

This is a local package: the command runs on your machine.

Quality – / 100not scored

Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.

protocoln/a · weight 25

n/a
protocol.modern, protocol.stateless, protocol.transport, protocol.list_ttlno remote answered a protocol handshake (not probed yet, unreachable, or local-only)

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygienen/a · weight 30

n/a
tools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)

stabilityn/a · weight 15

n/a
stability.changes, stability.rug_pulltool list unknown

dependencies100 · weight 15

pass
deps.known_vulnsno known advisory in 2 resolved packages
n/a
deps.mcp_sdk_versionthe official MCP SDK is not in the dependency graph
pass
deps.resolvable[email protected] resolved: 2 packages

Tool list unknown · checked 2026-10-20 16:30 UTC

Tool changes

No tool definition changes recorded. A server's first observation is its baseline; later probes record what changes.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 91 / 100

provenance90

livenessn/a

freshness85

hygiene100

+repository +namespace-matches-repo +website ~liveness-unmeasured ~updated-37d-ago

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

[email protected] npm1 dependencies, resolved · advisories checked 2026-10-19

No known advisory affects this dependency graph.

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

package	registry	version	runtime	secrets
`biomcp`	npm	1.4.3	npx	`NCBI_API_KEY`, `S2_API_KEY`, `OPENFDA_API_KEY`, `ONCOKB_TOKEN`, `DISGENET_API_KEY`

Tools (0)

No tools observed. Local packages are never executed by the registry.

Schemas: list_tools.

Similar MCP servers

Official server.json

{
  "name": "io.github.yeyuan98/biomcp-ts",
  "title": "BioMCP-TS",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "version": "1.4.3",
  "packages": [
    {
      "version": "1.4.3",
      "transport": {
        "type": "stdio"
      },
      "identifier": "biomcp",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "ANALYSIS_BIOWASM",
          "description": "Set to 1 to enable the samtools/bedtools/bcftools biowasm analysis tools"
        },
        {
          "name": "ANALYSIS_R",
          "description": "Set to 1 to enable the R/Bioconductor analysis tools (requires the webr peer dependency; use the pinned one-shot client command)"
        },
        {
          "name": "DB_TYPE",
          "description": "Set to mysql or sqlite to enable the read-only SQL database tools"
        },
        {
          "name": "NCBI_API_KEY",
          "isSecret": true,
          "description": "Higher NCBI E-utilities rate limits (3 -> 10 req/s)"
        },
        {
          "name": "S2_API_KEY",
          "isSecret": true,
          "description": "Higher Semantic Scholar rate limits"
        },
        {
          "name": "OPENFDA_API_KEY",
          "isSecret": true,
          "description": "Higher OpenFDA rate limits"
        },
        {
          "name": "ONCOKB_TOKEN",
          "isSecret": true,
          "description": "Required by the variant_oncokb tool (OncoKB annotations)"
        },
        {
          "name": "DISGENET_API_KEY",
          "isSecret": true,
          "description": "Required for DisGeNET disease-gene associations"
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/yeyuan98/biomcp-ts",
    "source": "github"
  },
  "websiteUrl": "https://github.com/yeyuan98/biomcp-ts/blob/main/docs/AGENT-INSTALL.md",
  "description": "Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools."
}