MCP server

Pombase

io.github.pipeworx-io/pombase

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

44

Token cost

About 26,640 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

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

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.pombase]
url = "https://gateway.pipeworx.io/pombase/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"pombase":{"type":"http","url":"https://gateway.pipeworx.io/pombase/mcp"}}}

Antigravity

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

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"pombase","server_url":"https://gateway.pipeworx.io/pombase/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"pombase","server_url":"https://gateway.pipeworx.io/pombase/mcp"}

Tools

• get_gene ~197 tokens
  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
• get_reference ~140 tokens
  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.

Browse

• GitHub tools
• GitHub and code hosting
• Databases
• Research papers

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