Reactome vs Wikipathways

In-depth architectural comparison of the Reactome and Wikipathways MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

R

Choose Reactome when:

• You need dedicated capabilities in the Databases domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Reactome Details

Choose Wikipathways when:

• You need dedicated capabilities in the Databases domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Wikipathways Details

Feature & Specification Comparison

Specification	R Reactome Databases	Wikipathways Databases
Summary	Reactome biological pathway database	WikiPathways MCP — open community pathway database.
Category & Scope	Databases	Databases
Quality signal

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "reactome": {
      "command": "npx",
      "args": [
        "-y",
        "reactome"
      ]
    }
  }
}

{
  "mcpServers": {
    "wikipathways": {
      "command": "npx",
      "args": [
        "-y",
        "wikipathways"
      ]
    }
  }
}

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