Koskamo

Wikipathways MCP

The Wikipathways MCP server provides tools to search, list, and retrieve metadata for biological pathways from the open WikiPathways community database. It allows agents to map genes, proteins, and metabolites to processes like glycolysis or apoptosis, supporting organism-specific pathway retrieval and detailed pathway metadata access.

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Package and access

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

Wikipathways MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • Search WikiPathways for biological pathways by name
  • List all pathways for a specific organism like human or mouse
  • Get metadata and viewer links for a specific pathway by ID

Source and maintenance

Community listingRegistry 0.2.0
mcp-registry: io.github.pipeworx-io/wikipathways@0.2.0Source repositoryProject website
Maintenance checked

Packages and installation

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

@pipeworx/mcp-wikipathways 0.2.0

npm
@pipeworx/mcp-wikipathways package definition
{
  "version": "0.2.0",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-wikipathways",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

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": {
    "wikipathways-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-wikipathways@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "wikipathways-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-wikipathways@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
    "wikipathways-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-wikipathways@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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": {
    "wikipathways-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-wikipathways@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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