A
license-
qualityC
maintenanceEnables querying disease/target/drug knowledge graph from Open Targets, supporting searches, profiles, and associations via natural language through the Pipeworx gateway.
18
MIT
mcp-wikipathways
by pipeworx-io
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@mcp-wikipathwaysfind pathways related to Alzheimer's disease"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
mcp-wikipathways
WikiPathways MCP — open community pathway database.
Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.
Tools
Tool | Description |
| Search WikiPathways (open community pathway database) for biological pathways by name. Pathways map genes/proteins/metabolites in processes like glycolysis, apoptosis, or signaling. Optionally restrict to one organism by Latin or common name. Keyless. Complements KEGG/Reactome. |
| List all WikiPathways pathways for a single organism. Give a Latin or common name, e.g. "Homo sapiens", "human", or "mouse". Returns each pathway's id, name, link, and last revision. Keyless. |
| Get metadata and a viewer link for one WikiPathways pathway by its WikiPathways id (e.g. "WP554"). Returns name, species, revision, and a human-viewable diagram URL. Keyless. |
Related MCP server: reactome-mcp
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"wikipathways": {
"url": "https://gateway.pipeworx.io/wikipathways/mcp"
}
}
}Or connect to the full Pipeworx gateway for access to all 1394+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Wikipathways data" })The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
This server cannot be installed
Maintenance
–Maintainers
–Response time
–Release cycle
–Releases (12mo)
Commit activity
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Looking for Admin?
If you are the server author, to access and configure the admin panel.
Related MCP Servers
reactome-mcpofficial
AlicenseBqualityFmaintenanceEnables AI assistants to search, browse, analyze, and export biological pathway data from Reactome through natural language.566Apache 2.0- Alicense-qualityCmaintenanceMCP server that wraps the Wikidata API, enabling AI agents to query and interact with Wikidata data using natural language through the Pipeworx gateway.9MIT
- Alicense-qualityCmaintenanceEnables AI agents to query the Reactome biological pathway knowledge-base for pathways, participants, and orthologous events using natural language.13MIT
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