BioMCP-TS

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