BioMCP-TS

Name: BioMCP-TS
Author: yeyuan98

yeyuan98

Democratizing Agentic Access to Bioinformatics and Biopharmaceutical Databases and Analyses with BioMCP-TS. Part of the BioResearcher Agent Suite.

Setup

Choose your client, copy the config, then fill in any required environment variables.

Add to Cursor Add to VS Code

claude mcp add biomcp-ts --env NCBI_API_KEY='<NCBI_API_KEY>' --env S2_API_KEY='<S2_API_KEY>' --env OPENFDA_API_KEY='<OPENFDA_API_KEY>' --env ONCOKB_TOKEN='<ONCOKB_TOKEN>' --env DISGENET_API_KEY='<DISGENET_API_KEY>' -- npx -y biomcp

~/.codex/config.toml

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

# codex mcp add biomcp-ts --env NCBI_API_KEY='<NCBI_API_KEY>' --env S2_API_KEY='<S2_API_KEY>' --env OPENFDA_API_KEY='<OPENFDA_API_KEY>' --env ONCOKB_TOKEN='<ONCOKB_TOKEN>' --env DISGENET_API_KEY='<DISGENET_API_KEY>' -- npx -y biomcp

~/.cursor/mcp.json

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

.vscode/mcp.json

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

~/.gemini/settings.json

{
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "biomcp"
      ],
      "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_desktop_config.json

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

.trae/mcp.json

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

Environment variables

NCBI_API_KEY
S2_API_KEY
OPENFDA_API_KEY
ONCOKB_TOKEN
DISGENET_API_KEY

Replace the placeholders with your own credentials and keep them out of version control.

Setup

Environment variables

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