{
  "slug": "io-github-yeyuan98-biomcp-ts",
  "name": "io.github.yeyuan98/biomcp-ts",
  "title": "BioMCP-TS",
  "description": "Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.",
  "version": "1.4.3",
  "publishedAt": "2026-09-14T02:34:23.993456Z",
  "updatedAt": "2026-09-14T02:34:23.993456Z",
  "repoUrl": "https://github.com/yeyuan98/biomcp-ts",
  "websiteUrl": "https://github.com/yeyuan98/biomcp-ts/blob/main/docs/AGENT-INSTALL.md",
  "namespace": {
    "type": "github",
    "owner": "yeyuan98"
  },
  "kind": "local",
  "packages": [
    {
      "registryType": "npm",
      "identifier": "biomcp",
      "version": "1.4.3",
      "transport": "stdio",
      "runtimeHint": "npx"
    }
  ],
  "remotes": [],
  "envVars": [
    {
      "name": "ANALYSIS_BIOWASM",
      "isSecret": false,
      "isRequired": false,
      "description": "Set to 1 to enable the samtools/bedtools/bcftools biowasm analysis tools"
    },
    {
      "name": "ANALYSIS_R",
      "isSecret": false,
      "isRequired": false,
      "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",
      "isSecret": false,
      "isRequired": false,
      "description": "Set to mysql or sqlite to enable the read-only SQL database tools"
    },
    {
      "name": "NCBI_API_KEY",
      "isSecret": true,
      "isRequired": false,
      "description": "Higher NCBI E-utilities rate limits (3 -> 10 req/s)"
    },
    {
      "name": "S2_API_KEY",
      "isSecret": true,
      "isRequired": false,
      "description": "Higher Semantic Scholar rate limits"
    },
    {
      "name": "OPENFDA_API_KEY",
      "isSecret": true,
      "isRequired": false,
      "description": "Higher OpenFDA rate limits"
    },
    {
      "name": "ONCOKB_TOKEN",
      "isSecret": true,
      "isRequired": false,
      "description": "Required by the variant_oncokb tool (OncoKB annotations)"
    },
    {
      "name": "DISGENET_API_KEY",
      "isSecret": true,
      "isRequired": false,
      "description": "Required for DisGeNET disease-gene associations"
    }
  ],
  "category": "databases",
  "subcategory": "sql",
  "company": "",
  "categoryAuto": true,
  "checks": [
    {
      "id": "source-linked",
      "label": "Source repository linked",
      "result": "pass",
      "detail": "https://github.com/yeyuan98/biomcp-ts"
    },
    {
      "id": "version-pinned",
      "label": "Version pinned",
      "result": "pass",
      "detail": "Every package has an explicit version"
    },
    {
      "id": "secrets-requested",
      "label": "Secrets requested",
      "result": "warn",
      "detail": "Asks for 5 secrets: NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY"
    },
    {
      "id": "known-registry",
      "label": "Known package registry",
      "result": "pass",
      "detail": "All packages come from npm, PyPI, OCI, NuGet or MCPB"
    },
    {
      "id": "namespace",
      "label": "Namespace ownership",
      "result": "info",
      "detail": "Name verified via GitHub account yeyuan98"
    },
    {
      "id": "meta-text",
      "label": "Registry text aimed at the AI",
      "result": "pass",
      "detail": "Description and settings contain no hidden characters or instructions to the AI"
    },
    {
      "id": "install-scripts",
      "label": "Install scripts",
      "result": "pass",
      "detail": "biomcp@1.4.3 runs nothing at install"
    },
    {
      "id": "code-flags",
      "label": "Code red flags",
      "result": "pass",
      "detail": "Read 8 files in biomcp@1.4.3: no obfuscation, encoded execution, credential reads or data-collection endpoints found"
    },
    {
      "id": "ai-text",
      "label": "Text aimed at the AI",
      "result": "pass",
      "detail": "No hidden characters or instructions to the AI in 8 files, including comments and the README"
    }
  ],
  "scannedAt": "2026-10-29",
  "level": "Scanned",
  "install": [
    {
      "label": "Claude Desktop (npm)",
      "kind": "claude_desktop_json",
      "text": "{\n  \"mcpServers\": {\n    \"biomcp-ts\": {\n      \"command\": \"npx\",\n      \"args\": [\n        \"-y\",\n        \"biomcp@1.4.3\"\n      ]\n    }\n  }\n}"
    }
  ],
  "curated": true,
  "stars": 12,
  "archived": false,
  "pushedAt": "2026-10-28T12:22:52Z",
  "health": {
    "score": 72,
    "parts": {
      "popularity": 0.4106599752106189,
      "activity": 1,
      "issues": 0.9404761904761905,
      "security": 0.8
    },
    "fail": 0,
    "warn": 1,
    "raw": {
      "stars": 12,
      "forks": 2,
      "downloads": 956,
      "hn": null,
      "issuesOpen": 5,
      "issuesClosed": 79,
      "prsMerged": 137,
      "commits90": 464,
      "release": "2026-10-26T14:09:23Z",
      "pushed": "2026-10-28T12:22:52Z",
      "growth": null,
      "growthDays": null,
      "archived": false
    },
    "at": "2026-10-31T07:42:38.200Z"
  }
}