Koskamo

ensembl-mcp-server

An MCP server that provides tools to query the Ensembl REST API for biological data. It allows agents to list species, look up genes by symbol or ID, fetch DNA/protein sequences, query genomic regions, predict variant consequences using VEP, find orthologs, and retrieve cross-database references like HGNC and UniProt.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

ensembl-mcp-server logo, by cyanheadsCommunity listingLocal stdioSource reviewed; not executedPublished by cyanheads
Vendor documentation

What you can do with it

  • Look up gene details by symbol or stable ID
  • Fetch DNA or protein sequences for genes
  • Predict functional consequences of variants
  • Find orthologs across species

Source and maintenance

Community listingRegistry 0.7.1
mcp-registry: io.github.cyanheads/ensembl-mcp-server@0.7.1Source repository
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@cyanheads/ensembl-mcp-server 0.7.1

npmnpx
@cyanheads/ensembl-mcp-server package definition
{
  "version": "0.7.1",
  "transport": "stdio",
  "identifier": "@cyanheads/ensembl-mcp-server",
  "runtimeHint": "npx",
  "registryType": "npm",
  "registryBaseUrl": "https://registry.npmjs.org",
  "environmentVariables": [
    {
      "name": "ENSEMBL_BASE_URL",
      "format": "string",
      "default": "https://rest.ensembl.org",
      "description": "Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror."
    },
    {
      "name": "MCP_LOG_LEVEL",
      "format": "string",
      "default": "info",
      "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<YOUR_ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<YOUR_ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "ensembl-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<YOUR_ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<YOUR_ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

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