How do I install Pombase?

Copy the http config for Cursor, Claude Desktop, Claude Code, or VS Code on this page. It uses the publisher's install, not a PlugMCP proxy.

Does Pombase need an API key?

The publisher lists these environment variables: PIPEWORX_API_KEY.

Pombase MCP server

Q: When was Pombase last checked?

Last checked 2026-11-10. PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.

Power your agent

Add this server

The publisher's own URL. Not a PlugMCP endpoint.

Add to Cursor Add in Claude Add to VS Code Run on PlugMCP

Host a copy with our keys and logs.

Server URL

https://gateway.pipeworx.io/pombase/mcp

Credentials from the publisher

PIPEWORX_API_KEY — Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap.

The Claude button above opens Claude with the name and URL filled in. You still confirm it there.

shClaude Code

1claude mcp add --transport http io.github.pipeworx-io-pombase https://gateway.pipeworx.io/pombase/mcp

Run in a terminal.

jsonClaude Desktop

1{2  "mcpServers": {3    "io.github.pipeworx-io-pombase": {4      "command": "npx",5      "args": [6        "-y",7        "mcp-remote",8        "https://gateway.pipeworx.io/pombase/mcp"9      ]10    }11  }12}

claude_desktop_config.json

Remote · HTTPPublisher installStep-by-step: add this in Claude

Remote URL or a command on your machine? How the two installs differ

Run on PlugMCP

Host a copy with our keys and logs.

A new server you create. It is not this listing's official endpoint. Use the publisher install when you want their URL and their credentials.

Launch

Server facts

Remote

Transport: http
Version: 0.2.1

Tools

No tool list yet. Remote servers get one after the first health check.

FAQ

Questions

mcp-pombase

PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.

Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.

Tools

Tool	Description
`get_gene`	PomBase (fission yeast / S. pombe model-organism DB): look up a gene by its PomBase systematic id and return its product, protein domains (InterPro), deletion viability, UniProt id, and curation status. Keyless. NOTE: requires a systematic id like "SPAC1002.01" or "SPBC2F12.13" — standard gene names like "cdc2" are NOT resolved by this API. Complements SGD (budding yeast).
`get_reference`	PomBase: look up a curated S. pombe publication by its PubMed id (e.g. "PMID:11739790") and return its title, citation, authors, year, abstract, and how many genes it annotates. Keyless.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "pombase": {
      "url": "https://gateway.pipeworx.io/pombase/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/pombase/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Both URLs reach the same gateway and the same 1683+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/pombase_get_gene \
  -H 'Content-Type: application/json' \
  -d '{"id":"SPAC1002.01"}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/pombase_get_gene. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "pombase": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-pombase"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-pombase

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Pombase data" })

The gateway picks the right tool and fills the arguments automatically.

License

MIT

Pombase

Add this server

Host a copy with our keys and logs.

Server facts

Tools

Questions

How do I install Pombase?

Does Pombase need an API key?

What transport does Pombase use?

When was Pombase last checked?

Documentation

mcp-pombase

Tools

Quick Start

What this endpoint actually serves

No MCP client? Call it over HTTP

Standalone (no gateway account)

Using with ask_pipeworx

More

License